The European champions - who lost the chance to regain their crown in midweek after going down to Deportivo La Coruna - looked like they were nursing a Champions League hangover.
Empoli's rearguard action stood firm for 85 minutes, until they conceded a penalty.
Italian star Andrea Pirlo (pictured) took the task on and he converted from the spot to give his side maximum points.
Roma made sure Milan's lead was not increased as they secured a comfortable 3-1 win.
John Carew opened the scoring after 29 minutes, before Federico Cossato levelled for Chievo just four minutes later.
The Roman giants then went ahead again on the hour when Antonio Cassano pounced and the points were secured 14 minutes from time when Andrea Barzagli put through his own net.
In the late match on Saturday, Juventus stayed a point behind Roma with a late 1-0 victory over Lazio at the Stadio delle Alpi.
David Trezeguet's fine downward header at the near post from Mauro Camoranesi's cross on the right gave the Bianconeri all three points in a match that had plenty of chances at both ends in Turin.
Already relegated Ancona grabbed their first win of the season with a 3-2 win over Bologna at Stadio Del Conero.
Hidetoshi Nakata had put Bologna ahead from the penalty spot after just 12 minutes, but then the home side pushed forward with attack verve they had been missing for the whole of the campaign up to this point.
Parma maintained their push for a Champions League with 3-1 win over Leece.
Benito Carbone slotted home after just 60 seconds for the home side, who then doubled their lead just before the interval through Alberto Gilardino.
Uruguayan Javier Chevanton then gave Lecce hope with his strike just after the hour, but Gilardino struck to seal the win.
Croatian Milan Rapaic levelled after 25 minutes and then Christian Bucchi put them ahead just after the interval.
Rapaic added a third soon after for Ancona and an Igli Tare effort (64) could not help Bologna as they slipped to a shock defeat.
Reggina remain in relegation trouble after losing 1-0 at home to Udinese.
The game was marred by a double sending off when each side were reduced to ten men with David Di Michele going off for the home side and David Pizarro seeing red for Udinese.
The only goal came just nine minutes from time when Vincenzo Iaquinta struck to give them the win - which keeps their Uefa Cup hopes very much alive.
Elsewhere, Siena were held to a goalless draw by Sampdoria, while Modena remain in the bottom four after drawing 0-0 with Brescia.
Click below for match summaries:
Serie A
AC Milan 1-0 Empoli
Ancona 3-2 Bologna
Brescia 0-0 Modena
Juventus 1-0 Lazio
Parma 3-1 Lecce
Reggina 0-1 Udinese
Roma 3-1 Chievo
Siena 0-0 Sampdoria
Click here for an updated Serie A table.
