The 21-year-old - a somewhat controversial omission from last year's World Cup finals squad - set up Ghanaian Kevin-Prince Boateng for Milan's second goal and then added a glorious third two minutes later to give them a five point lead over champions Inter Milan while Napoli are six points adrift of the leaders.
Swedish international striker Zlatan Ibrahimovic had opened the scoring for Milan early in the second-half from the penalty spot - a harsh call by referee Gianluca Rocchi for handball on Napoli defender Salvatore Aronica, who while the ball clearly hit his arm it did not seem to be deliberate on his part.
Milan coach Massimiliano Allegri said he believed from his viewing point that ROcchi had called it correctly.
"Seen from the sidelines it was a penalty," he said.
"But independent of that moment, Milan produced a good performance, and deserved the victory.
"We really played very well, (Christian) Abbiati didn't have to make a save and we created several chances.
"The thing that really pleased me was that the team was looking to make it 2-0, and even 3-0.
"The six point lead is a tidy advantage, but there are still a lot of matches to go, including the derby with Inter, and Napoli cannot be discounted yet."
Napoli - who exited the Europa League last week - gave few problems to Milan and the game went beyond them in the 77th minute when Pato found an onrushing Boateng and the World Cup star slotted the ball home to spark wild celebrations with the former Portsmouth player tearing off his shirt.
The 77,000 spectators were driven delirious with joy in the 79th minute.
Pato advanced with the ball, saw the Napoli 'keeper off his line and chipped into the far corner prompting once again huge celebrations with captain Gennaro Gattuso even mimicking his infamous headbutt on Spurs assistant coach Joe Jordan as he embraced Allegri.
Napoli found little in the final 10 minutes to raise their spirits as their two standout players this season Uruguayan striker and scorer of 20 goals Edinson Cavani and Slovakian playmaker Marek Hamsik failed to sparkle when it mattered most.
Milan travel to out of form Juventus, who have lost four of their last six matches, next Saturday.
Pato inspires Milan to crucial win over Napoli
Advertisement