There’s no simple answer to that, but I’d say it comes from a combination of factors.
The rain is the obvious one.
That year was the second where Toro Rosso and Red Bull were using the same chassis, as they used Red Bull technology to hold the IP. Remember that Toro Rosso actually finished ahead of Red Bull Racing that year. The car was fundamentally quick.
At Monza, Toro Rosso had an advantage over the parent team by using the more powerful Ferrari engine rather than the Renault.
It wasn’t just Seb who was fast. Webber qualified 3rd and Bourdais 4th. We never found out how well Bourdais could do because he stalled on the grid.
Variable rain levels in qualifying mixed up the grid further. Seb might have not won if Lewis had been near the front at the start.
The entire field was very close at the time. If you’re used to today where the top teams have a margin between them and the midfield, that wasn’t the case at the time. So at Monza, which like today is pretty unique on the calendar, swings in performance would be noticeable on the grid.
I’d say it was a perfect storm for Seb. Everything lined up for him that day, and all he had to do was get his head down and lap in clear air, which is his strength as the past decade has shown.