Berbatov was left out of the squad for the Barclays Premier League clash, with head coach Juande Ramos accusing the striker of having a negative effect on the dressing room and being distracted.
• Ramos plans talks with Berbatov
Sunderland took full advantage and led through Kieran Richardson's powerful drive, before Jermaine Jenas equalised.
However, Cisse - signed on loan from Marseille this week - headed in with seven minutes to go to inflict consecutive defeats for Spurs.
Ramos is clearly concerned with how Berbatov affects morale in his squad, but another problem he faces is the lack of strikers available.
A year ago Spurs had the four strikers they thought would fire them into the Champions League places, but only Darren Bent is left after Jermain Defoe and Robbie Keane left and Berbatov made it clear he wanted to join them through the exit door.
Middlesbrough were the beneficiaries of Berbatov's absence last week - he was a substitute at the Riverside - and Spurs missed his spark against the Black Cats.
Bent was prolific in pre-season but has struggled in his first two matches of the season and he barely had sight of goal in a dull first half.
David Bentley, playing as one of the attacking midfielders in a 4-2-3-1 formation, had the first effort at goal, but his 25-yard drive went well wide.
El-Hadji Diouf tried his luck from a similar distance for Sunderland, but Jonathan Woodgate headed the shot away for a corner. At the other end, Woodgate got his head on a Bentley corner but could not direct his header on target.
Attempting to make something happen, Gareth Bale earned a booking in the 26th minute for a dive as he tried to convince Mike Dean into awarding a penalty when Danny Collins challenged him in the area.
Roy Keane had Andy Reid and Steed Malbranque, both former Spurs players, in Sunderland's starting XI and both received warm receptions from the home fans.
It was Malbranque who came closest to opening the scoring in the first 45 minutes. The Frenchman struck the foot of the post six minutes before the interval with a low drive from long distance, with Woodgate clearing the rebound.
Bale had a clear opening three minutes after the restart when he met Bentley's corner, but his header went over Craig Gordon's crossbar.
Danny Collins also went close with his head for Sunderland when Reid found him with a free-kick.
Heurelho Gomes was then forced into a save when Daryl Murphy met Diouf's far-post cross with a volley.
The visiting fans were not made to wait long for the opener, with Richardson cracking his powerful half-volley perfectly.
Ledley King had failed to clear and then Richardson won a tussle with Jenas 25 yards from goal before unleashing his finish.
Spurs fans were still protesting for a handball as Richardson whipped off his shirt and ran towards the Sunderland fans.
Woodgate should have equalised when Gordon could only parry Bentley's free-kick - but the finish from the six-yard box went wide. Gordon also saved when Bent ran through and lashed at the near post.
Bentley had a shot tipped over by Gordon before the equaliser came with 17 minutes remaining. Luka Modric burst into the penalty area and after his shot was saved, Jenas tapped into the empty net.
Then an unmarked Cisse got on the end of Daryl Murphy's cross to score the winner and compound Spurs' problems.
Ramos plans talks with Berbatov
Tottenham head coach Juande Ramos will leave it to club officials to decide if
Dimitar Berbatov should be fined for not being in the right frame of mind to
feature in the defeat to Sunderland.
Berbatov handed in a transfer request just over a week ago and met with Ramos
on Thursday on his return from international duty with Bulgaria, and it was
decided he would not face Roy Keane's men in the Premier League clash
at White Hart Lane.
The 27-year-old will meet Ramos again tomorrow and could also face punishment
from his club.
'That is a decision the club has to make,' Ramos said. 'That is a very
interesting question you should ask the club.'
Berbatov's absence left Spurs with Darren Bent leading their attack, and they
suffered defeat courtesy of Djibril Cisse's 83rd-minute winner.
Kieran Richardson had given the visitors a 55th-minute the lead before Jermaine
Jenas levelled in the 73rd minute.
Predictably, Berbatov's absence took most of the attention.
Ramos had issued a statement before the game explaining: 'He didn't play
because he wasn't in the right condition, this is what he told me before the
game when I spoke to him. So he did not play.
'We'll have to wait and see, tomorrow we'll speak to the player and then we'll
make a decision (on his future).
'It's a situation that is very personal, there are players able to play under
these circumstances and others whose head is not right. Berbatov is in the
latter category.
'We'll have a meeting with the player and clarify a few points and see if
there is a decision to be made.
'We'll meet primarily to know if he is in any state to play in the next match
or we have to find another solution.'
Ramos argued that Berbatov, despite what some may see as effectively going on
strike, does not hold more power than the club.
'He hasn't got any power, if he is no condition to play the game he in not
going to play, that is the same as any other player.'
Sunderland boss Roy Keane refused to get carried away with the victory,
insisting: 'We won't be dancing in the streets in Sunderland for beating
Tottenham away from home, we'll have a cup of tea and sandwich as normal.
'We fancy our chances and we're happy with the progress we're making. Players
showed the other side to them.
'The character of the players is there for everyone to see. We have that and
you can criticise in other areas but not character.
'When you've won the game you say Berbatov's a talented boy but (Darren) Bent
is also a good player.'
Cisse headed home seven minutes from time to score the winner on his club debut
after signing on loan from Marseille this week.
Keane added: 'Someone told me he scored on his debut for Liverpool but I
couldn't careless what he did in the past.
'It's a good start. Djibril only trained with us yesterday and he was always
going to be on the bench, he gives us good options if things aren't going our
way.'
Tottenham Hotspur 1 - 2 Sunderland
