Bottas survived a mistake at the final corner with six laps to go, which resulted in him skipping across the chicane, to complete a Mercedes one-two for the second race in a row.
"The whole weekend has been incredibly strong", Hamilton said. "This track's the best track in the world".
A rampant Hamilton, who stormed to a record-extending 80th pole, could not resist a dig at his rival.
Vettel, who was back to 11th by lap 24 of 53, is 50 points behind Mercedes rival Lewis Hamilton with just four races remaining after Sunday.
"I do not interfere with technical decisions, but that for me was unacceptable", said the Italian.
"It's normal that it sometimes gets close but you need to always give the space and in that case I couldn't go anywhere and then we touched".
"I think there are still some important things to understand and learn about the auto".
Vettel was then promoted to fourth at the end of the first lap when Max Verstappen locked his front wheel going into the hairpin, ran wide and pushed Kimi Raikkonen off when rejoining the track, allowing Vettel to slip past his team-mate. Verstappen was subsequently given a five-second penalty for not returning to the track safely. He resumed in 19th place with a damaged auto.
It was as far as he could go and to be fair a valiant effort but his race was long gone just as his title attempt has fallen by the wayside over the last seven races.
As his chances of pipping Hamilton to a fifth F1 crown slip away, Vettel was still seething after the race.
More news: Meghan Markle's Latest Givenchy Look Featured Sheer Panels and a Leg SlitVerstappen continued without losing much time but Vettel spun to the back of the field and was now consigned to a long afternoon fighting back.
Ricciardo was now the man on the move, having moved from 15th to 10th before the safety auto.
As the defending world champion charges towards a fifth world drivers' title, we discuss the key moments in the race at Suzuka. Max Verstappen said on Saturday when asked if his P3 would interfere with the fight at the top.
Told by Red Bull team boss Christian Horner that the Ferrari mechanics might be looking for him in the pit lane, Verstappen shrugged: "That's not my problem, they were too aggressive".
Hamilton held his pole advantage at the start and kept Mercedes team-mate Valtteri Bottas at arm's length throughout the first stint, which was punctuated by a safety vehicle. Hamilton complained intermittently of hesitations from his power unit from the lead, but he had no discernable difficulty keeping a five-second gap to his teammate in second place.
This then became a bigger issue after a mistake by Vettel on his first hot lap of the session when the rain did eventually reach the track.
Carlos Sainz was 13th for Renault ahead of Williams driver Lance Stroll.
Sergio Perez stole best-of-the-rest honours in seventh after Racing Point Force India mugged Haas and Toro Rosso with a superior strategy.
The fresh-tyre advantage allowed them to jump Gasly, before Perez caught and passed Grosjean after a virtual safety vehicle called to deal with Charles Leclerc's stricken Sauber.
