The victory in the fifth stage - his second in three days - gave the 28-year-old Russian cyclist the edge in the overall standings as most of his rivals finished well behind in the uphill race which ended at 1,675 metres on Terminillo peak.
Tonkov, the 1996 Giro winner, completed the distance in 6hr 14min 58sec at an average speed of 21.329mph.
Leblanc rushed ahead 200m from the finish line, but Tonkov was quick to fight back and beat him. Leblanc lifted himself from fourth to second place overall, 41sec behind Tonkov.
"It was a tough stage because of rain," said Tonkov, who is competing in the race with a bandaged left wrist, following an accident last month. "I proved in good form. I'm glad to be at the top, but there's still a long way to go."
The race, which ends in Milan on 8 June, continues today with a 130-mile hilly stage from Rieti to Lanciano.Reuse content