The Peru international's only other goal for Blues since his summer move from Bayern Munich had been on the opening day of the season against the same opposition.
He struck 11 minutes from time to earn Avram Grant's side a fourth successive win despite again being decimated by injuries and African Nations Cup call-ups.
• Grant hails patient Blues
Chelsea seldom fired on all cylinders despite having more of the possession but would have been pleased with the contribution made on his full debut by £15million capture Nicolas Anelka.
Alex McLeish's side gave a performance as committed as the one which had seen them share the spoils with Arsenal at the Emirates Stadium last weekend with skipper Damien Johnson impressive in the middle of the park.
But the former Scotland boss must be concerned by the number of goals his side concede from set pieces as Pizarro was first to react for the winner to a corner from Juliano Belletti.
Chelsea winger Shaun Wright-Phillips needed early treatment after landing awkwardly on an ankle following an aerial challenge with Johnson and he eventually was replaced by Pizarro.
Chelsea enjoyed the bulk of the possession for the majority of the opening 45 minutes with Michael Ballack and Florent Malouda impressive.
Birmingham midfielder Fabrice Muamba became the first player to be yellow carded after 11 minutes for a mis-timed challenge on Ricardo Carvalho.
Ballack was over-ambitious in going for goal from fully 40 yards out after Sebastian Larsson fouled Ashley Cole and the ball dribbled through to home goalkeeper Maik Taylor.
City were on the back foot for the majority of the time and full-back Stephen Kelly got an important touch on a fiercely driven free-kick by Ballack across the face of goal.
Birmingham were finding space on occasions in behind the two Chelsea full-backs on the counter-attack but could not take advantage of the situations with the final ball letting them down.
But Cameron Jerome could have put Birmingham ahead after 38 minutes after a blunder by Cech.
Cech made a mess of his clearance which flew at pace towards Jerome and his instinctive header from 18 yards out hit the outside of the post.
Birmingham started to build up some momentum towards the interval and Jerome was twice more denied by blocks in front of goal from Cole and Alex.
Chelsea seemed rattled and unsettled by the aggressive approach of Alex McLeish's side, who left the pitch at half time to a standing ovation.
Anelka gave a glimpse of his class when dummying Johnson but he dragged his 20-yard shot wide.
Birmingham were now having almost as much of the possession as the visitors and a half volley from Larsson was not too far off target.
The Swedish international then saw a low cross from Kapo bobble off his leg and wide after it had taken a slight deflection off Cech.
Kapo was an increasing influence and one deft pass played in Jerome whose shot was blocked by Cech, although the City striker had strayed marginally offside.
Chelsea created their best opening to date after 68 minutes when Malouda played in Anelka who found himself with only Taylor to beat.
But Rafael Schmitz got across just to make a vital touch on his eventual shot and Taylor was able to make the block.
McLeish made a double substitution after 73 minutes with the injured Jerome and O'Connor replaced by newcomer McFadden and Mikael Forssell.
And McFadden was soon in the thick of the action, forcing Cech to beat away his low drive.
But with 11 minutes left all the home side's hard work was undone as Pizarro headed in Belletti's corner despite the efforts on the line of Larsson to keep the ball out.
Grant hails patient Blues
Chelsea manager Avram Grant praised the patience shown by his team before a late goal from substitute Claudio Pizarro earned them victory at Birmingham.Grant was aware that Alex McLeish's side had drawn at Arsenal and only been beaten by a single goal at Manchester United.
And the Blues had to overcome a dogged and determined performance from the home side before Pizarro headed in a 79th-minute corner from Juliano Belletti.
Grant said: 'Although the goal came late, we had the majority of the possession except for the 10 minutes at the end of the first half.
'We didn't create so many chances but still had two or three opportunities before we broke through.
'Birmingham played with a lot of spirit and determination and fought very well but we deserved the win.
'We were aware that Birmingham had picked up points against Liverpool and Arsenal this season and it was very important to win here. They had only lost 1-0 at Manchester United.
'It is very difficult to play against them. They know how to defend and make good counterattacks so you need to be patient against them.
'We were patient because in these games you don't get many chances - especially against them at their place.'
Grant was pleased to see Pizarro score his first league goal since netting in the 3-2 win over Birmingham on the opening day of the campaign.
He said: 'It was one of his best games. He did a very good job for us and deserved the goal. It was well taken.'
Grant believes his side already have the momentum to mount a title challenge despite missing half a dozen players through injury and being on African Cup of Nations duty.
He said: 'We have got momentum. We have won so many games in the last three months. Nobody thought these players would do it but we have carried on winning.
'We are waiting to get players back from injury and international duty but we are doing fine.'
The only downside for Chelsea was a first half ankle injury to winger Shaun Wright-Phillips which could make him doubtful for the midweek Carling Cup second leg clash with Everton at Goodison Park.
Grant said: 'It is not looking good but we will wait and see how things are. Shaun was very good last week against Tottenham and we are used to losing players who are in good form. We want him back as soon as possible.'
McLeish felt his side deserved a share of the spoils but again bemoaned his side's failure to deal with a set-piece which led to the goal from Pizarro.
The former Scotland boss said: 'We feel hard done by. But we can't feel sorry for ourselves. It was a great performance and the reaction of the fans at the end said it all.
'There is no doubt that we have rattled Chelsea. But at the end of the day we have nothing to show for our efforts. We haven't done our job in terms of man-marking in the box for the goal.
'We got punished again. Pizarro did the damage after a great delivery for the corner from Belletti.
'We have worked on set-pieces at both ends of the pitch since I came here and now we will have a look again. Again we saw the importance of what can happen if you get the right delivery into the area.'
McLeish is refusing to comment on transfer speculation although it is understood Manchester City striker Georgios Samaras could be the next new addition at St Andrews next week.
But of equal concern is the centre of defence and midfield where City would be stretched should they pick up a couple of injuries or suspensions.
McLeish said: 'We are looking at people and we hope to try and bring a couple in in the next couple of weeks. My policy is to say nothing until a deal is done.
'But I am trying to get a couple in. We have strengthened the forward line but we still need players in midfield and the centre of defence.'
Birmingham 0 - 1 Chelsea
