Vettel overtook Webber and then third-placed Romain Grosjean at Suzuka to claim his fifth straight race victory and move a step closer to securing a fourth consecutive World Championship.
It appeared that Webber would be Red Bull's best chance of overtaking Grosjean when the Lotus driver led, but the Australian was called into the pits three times compared to Vettel's two stops.
The retiring 37-year-old went on to pass Grosjean on the penultimate lap, but he has admitted that he was initially confused when his team called him into the pitwall on the third occasion, which allowed his German colleague to pick up more points in his chase of the title.
"I didn't think the battle was going to be with Sebastian at the end to be honest," he told reporters. "It was pretty much done when we didn't do enough damage on the three-stop against Seb's pace on the two. We tried to race Romain at the end and then in the end we switched to a three. So I was the meat in a sandwich trying to beat Romain on a two and then all of a sudden we've decided to do the three.
"I was a little bit surprised. I asked was it the right thing to do because I felt we could get to the lap we were looking to get to. Of course Seb was two or three laps longer, four laps maybe, but in terms of the target lap that we looked to get to the two-stop [window] I thought was achievable.
"But in the end Seb did a good race, the strategy worked out perfect. The three was not absolutely ridiculous but it's a bit more high risk and you've got to clear people obviously [on the track]. So piggy in the middle trying to do both and in the end we got it back to where we were in terms of position, but obviously Seb jumped both of us [Webber and Grosjean]."
Vettel now leads Fernando Alonso by 90 points in the drivers' standings, with 100 left to compete for this season, starting in India next week.