With Tottenham winning at Bolton, Chelsea are now five points behind them and Newcastle, who are behind the fourth-placed Londoners on goal difference only.
It means that with two games to go, Chelsea need an unlikely run of results to finish in the top four, and their only hopes of competing in the Champions League will be to go through as holders.
And if that were to knock out Tottenham or Newcastle, it would be hard on either of them.
Alan Pardew’s men have consistently defied the odds to punch above their weight at the top end of the table, and they did so again here.
It was like a reverse of the situation in Barcelona last week, when Chelsea pulled off an unlikely result with a combination of defensive resilience and stunning goals on the counter. For Chelsea last week it was Ramires and Fernando Torres, here it was Cisse, who looks to be the bargain of the season.
Torres, who had started like a man whose magic powers had been restored, showed little sign of repeating his goal in Barcelona or the hat-trick he scored against QPR on Sunday. The Spaniard was full of confidence initially but looked as deflated as his team-mates as the game wore on.
In the opening seconds Torres set up Raul Mereiles for a chance that went high over the bar, then tried to go past Tim Krul but was let down by a touch that was too heavy, and was fouled by Check Tiote, an offence that earned the Newcastle enforcer a caution.
But rather than be subdued, Tiote and his team-mates grew bolder. Having weathered Chelsea’s storm, with light rain starting to fall, they put a dark cloud over the Blues’ hopes of finishing fourth when Cisse scored his 12th goal since being signed in January.
The Senegal striker put Newcastle ahead in the 19th minute with a lovely goal. Davide Santon started the move with a weaving run in from the left, and when his pass reached Cisse, the striker took one touch with his left foot and smacked the ball powerfully past Petr Cech into the far corner with his right foot.
Chelsea were stunned. The confidence brought about by a 12-match unbeaten run started to evaporate, and without the experience of Frank Lampard, Didier Drogba and Ashley Cole, who were all rested ahead of Saturday’s cup final, Di Matteo’s side lost their composure.
While Newcastle were fast and furious, Chelsea looked disjointed again.
Newcastle continued to create chances as Hatem Ben Arfa started to weave his magic from midfield. Yohan Cabaye robbed Florent Malouda to set up Demba Ba before the striker’s shot was palmed wide of the post by Cech.
As half-time approached, Ba hit the bar as he ran on to a corner that was drilled to the edge of the box.
Di Matteo started making changes at half-time, sending on Juan Mata to replace the ineffective Daniel Sturridge, and within half an hour, Drogba and Lampard were on too. But it didn’t help Chelsea break down Newcastle, who lost Tiote on the hour when the Ivorian was taken off on a stretcher with a neckbrace, having had extensive treatment on the pitch.
But his replacement Ryan Taylor was just as effective in stifling Chelsea’s attacks. It was just like last week at the Nou Camp, with the visitors camped inside their defensive third and the home side unable to find a way through.
Fabricio Coloccini made one great headed clearance, but Davide Santon outdid him, diving across the goal to head John Terry’s header off the line.
But the final crowning moment was to come. Shortly after 10 minutes of stoppage time began, following Tiote’s injury, Cisse struck the killer blow for Newcastle. There seemed little danger when the ball dropped at his feet 25 yards from goal and wide on the left. But with extreme nonchalance, he hit a stunning half-volley with the outside of his right boot that dipped, swerved and sailed over Cech into the far corner of the net.
CHELSEA: Cech 6; Bosingwa 6, Terry 6, Ivanovic 6, Bertrand 5; Ramires 6,Mikel 6, Merieles 6 (Lampard 78); Sturridge 5 (Mata 46), Torres 6, Malouda 5 (Drogba 61).
NEWCASTLE: Krul 7; Perch 7, Williamson 7, Coloccini 8, Santon 7; Ben Arfa 8 (Obertan 89), Cabaye 7, Tiote 8 (R Taylor 67), Gutierrez 7; Ba 7 (Ameobi 74), Cisse 9.
Referee: M Halsey (Lancashire).