Leclerc held off threats from both Hamilton and Valtteri Bottas to secure Ferrari's first win at Monza since 2010, having to get his elbows out along the way.
Hamilton was forced to take to the escape route as he tried to overtake a stubborn Leclerc at the second chicane, with stewards opting to show Leclerc the black and white flag – F1's newly resurrected answer to a yellow card – rather than a time penalty.
"You have to judge him the same way as any other driver and this Sunday he did 'a Magnussen', that's the truth," Villeneuve told Motorsport-Magazin.
"When he made the move before the second chicane, at the most dangerous place - if that was on another track or if it was another driver, that would normally have been a penalty.
"He knew he could risk it, so he played with the limits and it worked for him."
Villeneuve was unhappy with the use of the black and yellow flag, which he believes will lead to drivers continuing to push what is permissible.
"It's like being allowed to do a stupid action in the race," he said. "They're going to start abusing it soon, depending on whether the yellow card is transferred to the next race, then of course the driver does not have that option."
Despite the criticism, Villeneuve credited Leclerc's ability to hold on to the end of the race as Mercedes flexed their strategy muscles.
He said: "It's great because he really did a great job, he was really strong, do not forget that he's only 21 years old.
"He was in control of the tyres until the end, that was all good, it was a great race finish."
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