Having been given inaccurate information that a rain storm was about to hit the circuit, Hamilton was left to rue a decision to stay on 'extreme' wet weather tyres during what was planned to be his one pit stop at Monza.
Had he switched to intermediate tyres the 23-year-old would have been able to mount a serious challenge to Vettel in his Toro Rosso. As it was, Hamilton had to pit again for intermediates.
"There was no chance of staying out on extremes, in the end it was damage limitation," he said. "I still had a great race. I passed eight others, including Kimi, which wasn't easy because it was very difficult out there. What happened was a bit of a shame, but I have still come away with my lead intact."
For once, though, even Hamilton's wet-weather mastery was eclipsed by Vettel, the charismatic German who at 21 years and 73 days became the youngest driver to win a Grand Prix.
Vettel had started from pole position, having won the qualifying lottery on rain-soaked Saturday, but few expected him to drive off into the distance to beat Heikki Kovalainen in the second McLaren by more than 12 seconds.
F1's new star is now destined for even greater things according to Toro Rosso team chief Gerhard Berger.
Having won the Italian Grand Prix himself 20 years ago, Berger said: "Sebastian proved he can win races. But he is going to win world championships, he is that good."
Vettel, who will replace the retiring David Coulthard at Red Bull next season, admitted he came close to tears standing at the top of the podium.
He said: "I saw the people down there, my team, my family, and they were going completely mad. Then to hear my national anthem was fantastic and I nearly started to cry. For sure, this was the best day of my life."
