The 35-year-old Vettel, who retires at the end of the 2022 season, started in ninth and proceeded to claim a sixth-place finish - this after spinning off on the first lap after making contact with Alpine's Fernando Alonso, which dropped the Aston Martin driver to the back of the field.
Following the red-flag period for the spin, and once the race restarted after a two-hour rain delay, Vettel was able to fight his way to a sixth-place finish on one of his favourite Formula 1 circuits at Suzuka.
In an interview following the race, which was shorted to 29 of the 53 scheduled laps due to wet conditions, Vettel said: "Obviously, it was a shame that we only got half a race but at least the people in the grandstands got to see some racing.
"We were waiting in the dry for the restart, but I imagine it must have been rather unpleasant to sit outside in the wet for a couple of hours.
"I got a very good start but then I collided with another car at the first corner. I really could not see anything. I am not sure, maybe I aquaplaned or I made a mistake but I lost all the positions I had gained and ended up last," Vettel said.
"When the race restarted, we made a good decision to box immediately for inters. It was a great stop, then I pushed like crazy and managed to undercut most of the field.
"It has been a dream weekend. For us to score eight points is a mega result.
"I feel sad to have driven my last race here, but it has been a wonderful weekend, and to all the fantastic Suzuka fans I can only say, 'Thank you'," he added.
Aston Martin boss Mike Krack said the timing of Vettel's pit-stop had played a big role for the team to get the great result, which has now lifted them to within seven points of sixth-placed Alfa Romeo in the constructors' standings with four races remaining.
"Once the race finally got underway, it was a great one, albeit not a long one," Krack said.
"But the main thing is it provided excellent entertainment for the always-enthusiastic Japanese fans who braved the wet weather to fill the grandstands, and for viewers all over the world who stayed glued to their TV sets despite the long hiatus in the on-track action.
"From an Aston Martin point of view, we scored our second consecutive sixth place, thanks to a fine drive by Sebastian, facilitated by a good strategy call to fit inters so soon after the restart and a superb pit stop that enabled him to exit the pit lane ahead of [Nicholas] Latifi."