Juve were a little sluggish to get going, but their ever-reliable talisman arrived to meet an Alex Sandro cross in the 38th minute to give Andrea Pirlo's side the lead.
Ronaldo looked hungry for more and another bullet header in first-half stoppage time doubled the lead, taking the Portugal forward back to the top of the league's scoring charts on 18 goals, one ahead of Inter Milan's Romelu Lukaku.
The 36-year-old had chances to complete a hat trick but it was Weston McKennie who added the third, hammering home his fourth Serie A goal of the season in the 66th minute from close range.
A first win in four matches in all competitions ensured Juve climbed from sixth to third in the table and onto 45 points, eight behind leaders Inter with a game in hand.
"The desire we have to return to the top makes me feel comfortable," Pirlo said. "The attitude of the players also pleases me.
"When we have more players free from injury I will have more choice and this also makes me feel comfortable. We know that Inter are a great team and we know we have to fight [to win the title]."
Crotone remain rooted to the foot of the table with 12 points from 23 games, eight points from the safety zone.
Aaron Ramsey thought he had given Juve the lead with a looping header only to see the ball hit the bar before Ronaldo showed him how it is done with two expertly-taken headers.
Ronaldo's goals mean Crotone are the 78th different team he has scored against in Europe's top five leagues -- only Zlatan Ibrahimovic has scored against more sides since 2000.
A glaring miss at the end of the half showed Ronaldo is only human, before two fine saves by Alex Cordaz after the break denied the Portuguese another hat-trick.
McKennie's close-range finish put the game beyond doubt, but league-leading scorer Ronaldo tried everything he could until the last minute to add more to his tally.