Crugnola, the 2023 winner and defending Italian champion, began leg two leading Boštjan Avbelj by 0.8sec after he went quickest of the ERC contenders through the Colosseum super special stage on Friday evening.
But a faster time from Avbelj on SS2 allowed the Slovenian to cut that gap to 0.1sec.
However, Crugnola responded on the 28.74km Santopadre - Fontana Liri stage to beat new second-placed driver Simone Tempestini by 2.7sec after Avbelj slipped back.
“I was trying to drive at my pace,” said Crugnola. “There was something in the car that was okay, I’m pretty much happy with my stage.
ERC champion Hayden Paddon is third behind Tempestini with Avbelj fourth, Simone Campedelli fifth, Mathieu Franceschi sixth, Efrén Llarena seventh and double ERC champion Giandomenico Basso eight.
Andrea Mabellini is ninth for Team MRF Tyres despite a heavy hit when he went wide on a right-hander during SS3. Roberto Daprà completes the top 10 heading to stage four.
Argentina-born Italian Fabio Mezzatesta retired after he was forced to stop on the road section to SS3 with a second damaged tyre. Hungarian champion Ferenc Vincze reported a loss of brakes halfway through SS3, an issue Jon Armstrong also experienced.
The 11.58km Guarcino - Altipiani test is due to get under way at 11:41 local time.