But Vettel seemed less concerned about the jeers than Webber.
"The more booing we get the better we've done today," Vettel said. "I don't blame the people to be honest, it's in their genes. They love Ferrari."
Webber's previous best finish at Monza was sixth place in 2010, also with Red Bull.
"It was good. We had a team weekend from start to finish, and then (fought) for the top position," Webber said. "Both Sebastian and I, compared to the Ferraris, were not that strong off the (start) line."
Webber went from third on the grid behind Ferrari's Felipe Massa, and lost his place to the Brazilian before reclaiming it and then chasing down Alonso.
"Got the job done against Felipe and it was a good battle with Fernando. Tried everything," Webber said. "We pushed as hard as we could and I'm satisfied with today's result."
Although Webber has only seven races left in his F1 career, the reality that it is coming to an end has yet to hit home.
"I think Brazil will probably be a little bit more emotional of course, but if I've got the tissues out then I've made the wrong decision," said Webber, who has won nine career races. "I'm not retiring (altogether). I'm stopping from Formula One but of course there are a lot of people that can come and watch me in the Porsche next year, at Le Mans and some other races."