Substitute Bojan Krkic opened the scoring in a scrappy game before Giampaolo Pazzini doubled Milan's lead. Siena sub Michele Paolucci pulled one back for the visitors but the Rossoneri held on to make a winning return after the winter break.
Kevin Constant came close to inadvertently opening the scoring in the third minute when his misplaced cross almost got the better of Gianluca Pegolo, the Siena stopper having to back-peddle quickly in order to tip the left-back’s centre behind for a corner.
Pazzini was then inches away from connecting with Riccardo Montolivo’s free kick before Stephan El Shaarawy squandered the best chance of the half. Serie A’s top marksman was given the type of opportunity he usually thrives on as the Siena defenders backed off and allowed the striker to dart into the box unchallenged. However, El Shaarawy was to be thwarted on this occasion by the bravery of Pegolo, the keeper diving at the feet of the oncoming attacker to divert his effort wide for a corner.
In an untidy half of football Milan struggled to assert themselves against Serie A’s weakest team and their visitors even enjoyed their own spell of relative dominance, forcing a series of corners before Simone Vergassola fired their only meaningful effort straight at Christian Abbiati from the edge of the area.
The match’s scrappy nature owed much to the persistent fouling from both sets of players and the inability of referee Gianpaolo Calvarese to award any form of advantage throughout, Mariano Angelo’s needless booking epitomising a forgettable 45 minutes.
The beginning of the second half hinted at bringing a bit more life into a flat San Siro and it was Siena who threatened to administer the much needed opening goal.
The visitors mounted one of their rare attacks down the left-hand side through Cristiano Del Grosso and his cutback fell to the feet of Alessandro Rosina, whose effort had to be beaten away by Abbiati.
Spurred into life by the prospect of falling behind, the home side turned to Kevin-Prince Boateng in their attempts to create anything that could break down the Bianconeri’s defence.
The first opportunity created by the Ghanaian attacker should have seen Milan take the lead. Boateng was found by Montolivo’s cutting through-ball and his cross was met by El Shaarawy at the back post, but the tricky forward could only head his effort back across the face of goal and behind for a goal kick.
Boateng was to be involved minutes later however when the Rossoneri finally broke the deadlock in somewhat controversial circumstances.
Some of the Siena players had stopped when Erjon Bogdani appeared to be fouled on the halfway line but with the referee not taking any action, Boateng picked up the ball and drove forward to deliver an inch-perfect cross for substitute Bojan to head home from the edge of the six-yard box.
Their lead was doubled with just 10 minutes left when Felipe needlessly nudged Pazzini inside the box and the former Inter man picked himself up to lash the penalty into the roof of the net.
However, Siena weren’t finished and substitute Michele Paolucci met Angelo’s cross to power a header past Abbiati and set up a tense finale which the home side survived to move to within five points of third-placed Fiorentina.