Paulo Dybala scored after just 44 seconds, with a Filip Bradaric own-goal accounting for Juventus' second after 39 minutes, two minutes after Joao Pedro had pulled the Sardinians level.
Ronaldo failed to add to his seven-goal league tally for new club Juventus with the Portuguese superstar hitting the woodwork before next week's Champions League visit by former club Manchester United.
But the 33-year-old's pass across goal set up Colombian Juan Cuadrado for his first of the season three minutes from time in the Allianz Stadium.
"He has always been a leader and an extraordinary player, as you saw from the assist he put on Cuadrado's foot," said Allegri. "These are different players who in the decisive moment always come up with a goal or a great pass."
Juventus have 31 points from 11 games with Inter and Napoli both on 25 points.
It is the best ever start to a season for the Turin giants who have drawn just one game against Genoa.
Earlier, Inter Milan crushed Genoa 5-0 to reclaim second spot on goal difference ahead of Napoli, who had eased past Empoli 5-1 on Friday, and keep the pressure on the seven-time reigning champions.
But Allegri insisted: "This isn't good enough. We have to defend better, we concede too many goals and risked letting in an equaliser in the 85th minute. Even after the first goal we didn't add a second and drifted out of the game. We can't always assume that we'll score two or three goals."
Wins by the top three were a boost before next week's Champions League fixtures, with Inter Milan at home against Barcelona and Napoli hosting Paris Saint-Germain.
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