The 21-year-old, who scored in both of Brazil's friendly victories during the international break, owed much to strike partner Zlatan Ibrahimovic for setting up his efforts.
First Pato expertly volleyed in a delicate Ibrahimovic cross from the left after 18 minutes, sending the ball back across the goalkeeper having patiently waited for it to drop.
Ibrahimovic then took a quick free kick on the half hour with the Chievo defence asleep and Pato blasted home to send a warning to Tuesday's Champions League opponents Real Madrid.
"I'm just doing my job, a job for the team. I'm happy with my two goals," Pato, who has again struggled for fitness this term, told Sky television.
Milan's most famous Brazilian, Ronaldinho, again had a quiet game in his new position behind the strikers rather than on the left although he did have two late shots.
In Saturday's other Serie A game, last term's runners-up AS Roma recorded only their second league win of the campaign with a nervous 2-1 victory over Genoa at the Stadio Olimpico.
Former Genoa striker Marco Borriello, who earlier hit the post, opened the scoring when he prodded in Francesco Totti's deflected cross before Matteo Brighi showed bravery to make it 2-0 after the break.
