كتب : Hatem Maher
Turkey were trailing 2-1 with three minutes remaining when Nihat capitalized on a dreadful error by goalkeeper Cech to draw Turkey level.
The Villarreal striker sent Turkey fans into raptures just two minutes later after scoring the winner.
Czech Republic had earlier led through Jan Koller in the first half and went further ahead via Jaroslav Plasil in the second period.
Turkey forward Arda Turan narrowed the deficit before Nihat's late show condemned the Czechs to a painful defeat.
Turkey progressed to EURO quarter-finals as Group A runners up with six points.
Portugal, who suffered a 2-0 defeat to Switzerland, have the same amount but advanced as the group winners due to superior head-to-head record over Turkey.
Czech Republic took a deserved lead in the 34th minute when Koller connected with a right-wing cross from Zdenek Grygera to power a header past Volkan Demirel.
The 1996 runners-up continued pressing forward in the second half and wasted several clear-cut opportunities to extend their advantage.
The clearest chance fell to Koller two minutes past the hour mark.
The Nurnberg towering striker latched onto a long ball to beat the offside trap and go clear on goal but he dragged his shot wide of the post.
Plasil made amends few moments later when he slide home at the far post after meeting Libor Sionko's cross.
Jan Polak was unlucky not to score the third in the 71st minute when his close-range effort was denied by the post.
The Czechs were made to pay for the miss four minutes later after Turan received Hamit Altintop's neat cross with a low drive that went into the net although Cech got a hand to it.
Nihat stole the show late in the game. He grabbed the equalizer for Turkey in the 87th minute, thanks to Cech's blunder.
The Chelsea guardian saw a tame cross slip out of his grasp. Nihat pounced to slot home into an empty net.
The former Real Sociedad man notched the decisive strike one minute from time.
He ran onto a deft pass to break the offside trap and fire into the roof of the net past Cech, who had a night to forget.
Turkey finished with ten men after keeper Demirel was shown a straight red card for an off-the-ball push on Koller