Mercedes's manipulation was controversial but Bottas, who is out of the championship fight with five races remaining, said: 'I am prepared to play for the team.
Bottas was the first of the frontrunners to head into the pits on lap 12 and was followed by Vettel on the next lap.
Bottas said the decision was "confusing" and that he was not prepared for it.
"It's honestly the strangest day I can remember having in the sport in my career", said reigning world champion Hamilton.
"We have a strong package going into the weekend and should be quite competitive there, so I hope that we will be able to see some good results and score more points." .
"Today the feeling with the auto was very good and I was able to push, but I just wasn't as fast as the others", said Vettel. "It would have been a race win for him and we changed it". He would lose second place to Sebastian (Vettel) and that wouldn't be ideal for both of the championships, so I think that was the worry but I think in the end it proved that actually it wasn't that bad.
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Bottas waved Hamilton through, allowing him into the lead, and also allowing him to collect 25 points in the process.
With the uncanny ability of Lewis to put his vehicle on pole, and that of Bottas to pull out the occasional superb lap, we believe that Ferrari's underdog story this season will continue as Vettel & Raikkonen will be forced to fight from underneath in order to make their way up through the ranks and take the victory on Sunday.
On the main straight the next time around, Hamilton believed that Vettel had defended his position with a double move.
Bottas did secure the fastest lap of the race late on as he and Hamilton pushed in the closing stages but said it meant nothing.
"Suzuka will be another challenging weekend for us", declared Mercedes F1 boss Toto Wolff, whose team are 53 points clear of Ferrari in the constructors' standings.
"Rationally, it was the right decision, but our sporting heart says no".
Naturally, in the midst of a tight championship battle with Ferrari, the decision was taken from a team perspective.
The 33-year-old got the win after he was allowed to pass by Valtteri Bottas on the orders of Mercedes.