The defender inadvertently turned Kevin-Prince Boateng's cross past goalkeeper Nicola Pavarini, five minutes before the end of the first half, before the Rossoneri striker fired into the top corner to earn all three points for the hosts, regardless of the late consolation from Nicola Sansone.
The hosts enjoyed the better of the early possession after Kevin Constant broke through the Parma midfield. He played in Balotelli, but the Italian saw his effort deflected behind for a corner.
Milan continued to press in a bid to net an early opener at San Siro. Boateng saw a low drive held comfortably by Parma goalkeeper Pavarini, before Rossoneri centre-back Mario Yepes forced a save out of Christian Abbiati having inadvertently turned a header towards his own goal.
Parma looked to take advantage of the shaky Milan defence after a poor Cristian Zapata clearance was capitalised upon by Paletta. The defender skipped past Yepes, but dragged his effort wide of Abbiati's goal.
The game slowed until the 25th minute as Amauri managed to beat Yepes to a Marco Marchionni corner and head goalwards, only to see his effort well saved by Abbiati, before Marchionni attempted a spectacular half volley from 30 yards that drifted over the bar on the half hour mark.
At the other end, Balotelli played in Boateng on the left of the 18-yard box with a perfectly weighted reverse pass as the Milan midfielder played across the box, but could not pick out the outstretched leg of M'Baye Niang at the far post. The creator then almost turned goalscorer after Mattia De Sciglio's cross was headed into the path of the Ghanaian by Djamel Mesbah, but his effort was weak and saw Pavarini gather easily.
Milan seized the initiative with five minutes remaining of the first half as Paletta mistakenly turned Boateng's low cross past Pavarini and into the back of the net.
Sully Muntari should have doubled the hosts' advantage just five minutes after the restart following some good work by Niang on the right, but the midfielder could not guide the cross past Pavarini. Balotelli then picked out Boateng moments later with a perfect low pass, only for the midfielder to side-foot his effort just wide of the Parma goal.
Balotelli saw a free kick blocked by the wall with half an hour remaining, before launching a venemous half volley towards goal that drifted wide for a goal kick.
Amauri failed to turn a Jaime Valdes ball over the top goalbound, while at the other end Antonio Nocerino looked to capitalise on a poor Pavarini clearance, but fired his speculative effort wide.
With 15 minutes remaining, Balotelli ensured the points were secured after firing a free kick past Pavarini and from 30 yards out, doubling his side's advantage.
Riccardo Montolivo came close to adding a third in the dying embers of the encounter, only for the Parma goalkeeper to deny the midfielder, before Balotelli tested the Crociati man inside the 18-yard box.
Parma netted a late consolation through Sansone, but it was too little to late as Milan hung on for all three points.