With this win, the side extended their lead at the top of the table by 11 points as Napoli drew against Fiorentina.
The Old Lady are at the top of Serie A and have not lost a match in the league this season.
"We could have played with Dybala and Cristiano but we needed a team with more balance", Allegri said.
Juventus have had a couple of shaky games in the last few weeks, which include a 3-0 loss to Atalanta in the Coppa Italia.
"To play like this, everyone needs to contribute, but we should also compliment the team for how they dealt with the game".More news: Kamala Harris: I’ve Smoked Weed and ‘I Did Inhale’
Since moving to Turin from Real Madrid in a €100million (£88.5m) move last summer, the 34-year-old Ronaldo has scored 18 goals in 23 league appearances, and 20 in 31 appearances in all competitions overall. Dybala is playing the same role as he did last year and the year before.
Milan's opener was an own-goal as Cagliari goalkeeper Alessio Cragno parried Suso's effort and it came off teammate Luca Ceppitelli.
Khedira scored his second goal of the season in the 23rd minute to put Juve in front and committed displays from Blaise Matuidi and Federico Bernardeschi ensured Massimiliano Allegri's men did not miss Paulo Dybala, who was named on the bench after he stormed off the touchline against Parma.
It was Piatek's fourth goal in three starts for the Rossoneri but Paqueta's first for Milan and he dedicated it to the victims of the fire at the training ground of his former club Flamengo.
"It was a very hard time for me", said the 21-year-old.More news: Pakistan PM Imran Khan’s remark on minorities an insult: Government
The side from Bergamo battled to a 2-1 win over SPAL, with Roma beating Chievo 3-0 and Lazio seeing off Empoli 1-0 during the week.
Messi was not at his best and neither was Barcelona, which would even have lost had it not been for Marc Andre ter Stegen's stunning late save to deny Inaki Williams.
Earlier, Atalanta, briefly moved into the Champions League places with a 2-1 win over SPAL - the in-form Duvan Zapata netting their victor with his 18th goal in 12 games.
Premier League (On Sunday): Manchester City 6 (Sterling 4, 80, Aguero 13, 19, 56-pen, Gundogan 25) bt Chelsea 0.More news: Saudis don’t know where Khashoggi’s body is