The five-time world footballer of the year failed to get on the scoresheet but laid on each of the Bianconeri's three goals in their 3-1 success.
A seventh straight Serie A win for Juve means they are now six points clear of second-place Napoli – a lead that could be reduced to five on Sunday should Sassuolo continue their fine start to the season by beating AC Milan.
Napoli took an early lead through Dries Mertens, before Ronaldo delivered a stunning cross for Mario Mandzukic to head home an equaliser.
Ronaldo's shot then cannoned back off the post for the Croatian striker to double his tally before the former Manchester United man headed a late corner into the path of Leonardo Bonucci to add gloss to the scoreline.
While the 33-year-old missed a number of opportunities to score himself, his coach thinks he should be content with a fine display.
"Cristiano Ronaldo? He did very well today and he created many clear cut chances for us," Allegri told Sky Sport Italia.
"Ronaldo has been doing very well for us and he really did some amazing things today.
"I think that this was his best game yet for us."
Juve's cause was aided in the 58th minute when Mario Rui received a second yellow card for an ugly foul on Paulo Dybala, but Allegri was furious with his side's reaction to the defender's dismissal.
"Once Napoli went down to 10 men, we stopped playing, and that made me angry," he added.
"We ran a big risk on Jose Callejon's chance and they could easily have equalised.
"We need to be sharper. Playing out from the back, we misplaced a pass and conceded a goal."
Allegri was also quick to play down suggestions that the reigning Italian champions will canter to an eighth consecutive league title, saying: "After this, we still have to play Inter, Milan, Roma and Fiorentina.
"We've got a six-point advantage, but it's a very long season. Also, Serie A is always tough."