Genoa and Sampdoria drew 1-1 in their derby and a blunder by Palermo goalkeeper Stefano Sorrentino, who appeared to forget the backpass rule, cost the relegation-threatened Sicilians a precious win against Bologna in another 1-1 draw.
Flamini fired Milan ahead in the 29th minute at San Siro and Goran Pandev replied four minutes later as a scrappy game briefly came to life, before fizzling out in the second half amid a glut of niggly exchanges.
The worst of them involved Flamini who lunged at Juan Camilo Zuniga with his studs up and was sent off amid pushing and shoving between the players.
The point improved Napoli's chances of a Champions League group stage place next season but reduced their hopes of catching leaders Juventus, who have 71 points and are eight clear with a game to come at Lazio on Monday.
The draw was not much use for Milan (59 points), who stayed four points behind Napoli in third and, with only the top two going straight to the Champions League group phase, look increasingly likely to face the uninviting prospect of a play-off tie in August.
Milan, missing suspended forward Mario Balotelli, also have to look over their shoulders at fourth-placed Fiorentina, only four points behind them after a 2-0 win at Atalanta on Saturday.
Cagliari's Mauricio Pinilla won and converted a 63rd-minute penalty after he was caught by Matias Silvestre in what appeared a harsh decision and the Chilean also scored the second to hand Inter their fourth defeat in five league matches.
Inter complained last week that they had not been awarded a penalty for 21 matches and club president Massimo Moratti said referees were not acting in good faith.
Inter's complaints were criticised by other clubs including neighbours AC Milan but coach Andrea Stramaccioni blamed injuries rather than the referee for his side's latest slip.
"The referees are making mistakes but they are repeating them," he told RAI television, adding that an injury to midfielder Walter Gargano upset Inter's balance. "The penalty was completely non-existent."
Inter, almost certain to be without Champions League football again next season, dropped to seventh with 50 points from 32 games.
Cagliari played the match in Trieste, nearly 1,000 km from their Sardinian base, due to security problems at the Is Arenas.
A speculative cross-shot by Matuzalem in the 80th minute gave Genoa a point against Sampdoria, who had taken the lead in the first half with a free-kick by his fellow Brazilian Eder which went under the defensive wall.
Sampdoria had Andrea Costa sent off for a second bookable offence just before the equaliser.
Palermo went ahead with a fourth-minute goal by Josip Ilicic but Bologna levelled in bizarre circumstances.
Sorrentino moved to pick up Michel Morganella's backpass, changed his mind, the ball went underneath h
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