Championship leader Verstappen claimed his first win at Monza and his fifth GP in a row after fighting from seventh on the grid to finish Charles Leclerc on another difficult day for Ferrari.
The race ended with jeers from the crowd and Ferrari frustration as the drivers had to finish the final six laps with the safety car after Daniel Ricciardo lost his engine and ended up at the side of the track.
However, Red Bull's Verstappen is 116 points ahead of Leclerc in the drivers' standings and can retain his crown in Singapore next month after winning his 11th race of the season, one he largely controlled despite being hit with a grid penalty on Friday.
"It was unfortunate, everyone wants to finish under a green flag, but unfortunately we were short of laps," Verstappen told reporters.
"But I had new softs so I wasn't too worried."
The massed ranks of red in the stands loudly voiced their disapproval when the cars came over the line as they were denied the chance to see their man Leclerc try to overtake dominant Verstappen, who was also booed on the podium by Italian supporters.
"The end was frustrating, I wish could have had a bit of racing at the end, unfortunately, we were second because of what happened before," said Leclerc.
The Monegasque lost out to Verstappen despite starting on pole but said after the race it had been "a positive weekend overall" despite Ferrari's plan of changing from soft to medium tyres during an early virtual safety car backfiring.
"I think we all had the doubt, I think if I hadn't done it Max would have done it," said Leclerc.
"It was a bit unfortunate because in the middle of the pit lane we have the virtual safety car ending so we didn't have any of the benefits of stopping at that moment and from that moment we were on the back foot."
George Russell of Mercedes rounded off the podium, while Leclerc's teammate Carlos Sainz surged from 18th on the starting grid to fourth.