Floccari shook off his marker, veteran Paolo Maldini, and saw his first effort saved by Australian goalkeeper Zeljko Kalac, but he was alert enough to flick home the rebound from a tight angle on 32 minutes.
Ten minutes later and Atalanta doubled its lead as a brilliant piece of control from Floccari, who then fed Antonio Langella.
He kept his cool to flick the ball over the onrushing Massimo Oddo's lunging challenge and then calmly side-footed home.
Milan had the ball in the net early in the second half but veteran Dutch midfielder Clarence Seedorf's effort was rightly ruled out for offside.
Atalanta should have made the game safe midway through the half, but after a fine break from Ferreira Pinto, Cristian Doni woefully skied his shot with the goal at his mercy.
Massimo Ambrosini then had another Milan strike harshly ruled out for a foul on goalkeeper Ferdinando Coppola.
Maldini scored with a header five minutes from time and Andrea Pirlo had the chance to snatch a point for the host in the last minute after Ambrosini was felled in the box. But he saw his penalty saved by Coppola.
Milan remains four points behind Fiorentina in the race for the crucial last Champions League qualifying position but it has lost its last two home matches and only the Viola's own stuttering form is keeping it in with a faint hope.
Udinese's victory actually moved it up to fifth, a point ahead of Milan, while Sampdoria, seventh after a 2-0 win at Empoli, is behind Milan only on goal difference - making it a four-way battle for the last Champions League spot.
"It's a very, very delicate situation," said Fiorentina coach Cesare Prandelli. "It's a very difficult position to be in but all our work is going toward finishing fourth."
On Saturday leader Inter Milan and second-placed AS Roma were both held to 1-1 draws.
Roma came back from the disappointment of conceding an early own goal through Matteo Ferrari to level matters at Cagliari with a Francesco Totti freekick.
Its cross-city rival Lazio then did Roma a favor by hitting back through Tommaso Rocchi after Hernan Crespo had given Inter the lead at Rome's Stadio Olimpico.
(Agencies via China Daily April 1, 2008)