Bottas was unable to improve his poor conversion rate from the front spot on the grid, as Hamilton extended his lead over the Finn to 85 points with four races to go.
Hamilton slipped from second to third behind Max Verstappen at the start, but the runaway Formula 1® championship leader put the hammer down at the front when he was kept out for a long opening stint on medium tyres.
Bottas was leading when he pitted just after Verstappen, both having hard compounds fitted, and Hamilton built up a big lead before a virtual safety car was deployed.
That made it very much advantage to the six-time F1® world champion, who took the chance to pit and secured victory ahead of Bottas following a restart with six laps to complete, after a late safety car was required when Verstappen spun off with a puncture.
Bottas' car suffered floor damage from debris on the Imola track, but he was able to secure second place after Verstappen's misfortune as the Silver Arrows wrapped up a record seventh consecutive constructors' title.
With Hamilton on the brink of winning a record-equalling seventh drivers' title, Bottas was left to reflect on what might have been, and he now has just five wins from 15 poles.
Bottas said: "I think [the damage to his car] made quite a big impact today. The start was good, that was one of the main things to get right today.
"Out of Turn Seven there was the debris, I didn't have time to avoid it - I saw it in the middle of the car, I tried not to run over it with the tyres but obviously it caused some damage that made the car tricky to drive.
"I was pushing hard to avoid Max getting through. I had to push over all of my limits which led to a few mistakes. Unlucky."
Renault's Daniel Ricciardo was able to celebrate third place in the first F1® race at the famous Italian circuit since 2006.