Lewis Hamilton went on to take full advantage by winning the race to extend his championship lead to 59 points but when asked about Ferrari's recent reliability record, Vettel replied: "I think I need to protect them".
Ferrari was forced to change a spark plug on Vettel's auto on the grid after finding an issue, only for the German to report a lack of power soon after the race starting.
He first lost a place to Max Verstappen at the hairpin and then Esteban Ocon, before falling down the field.
The current result places Hamilton in the title lead with a total of 306 points, 59 points clear off Vettel who is second with a total of 247 points.
Hamilton, who started the Japanese grand prix from pole position, can clinch the 2017 title at the USA grand prix in Austin later in October.
"The track was fantastic and the team did a sensational job, said Hamilton. I've just got to try and keep my head down and hopefully continue to perform like this".
"The team did incredible job, Max drove an outstanding race. I owe it to everyone that's here and back at the factory".
Maria likely to become tropical storm Tuesday night or Wednesday: NHC
Klotzbach said Lee becoming a major hurricane doesn't mean much for the rest of the season as far as number or strength of storms. Wave heights along the shore will increase during the next few days, creating unsafe surf and increased chances of rip currents.
Vettel's early retirement put a serious dent in his fading hopes of coming back to win the championship. It is good to get some rest and then we know we have the package to do well in the last four races.
A start-line crash in Singapore has been followed by engine problems at consecutive races in Malaysia and Japan.
"I'm reasonably happy", said the Ferrari driver. "I was always with Lewis and especially the last few laps we had great pace", he said.
"I think it is unbelievable really to think that we are where we are".
Ricciardo took third place, a further eight seconds back, while Bottas recovered from his gearbox penalty on Saturday to finish fourth.
"If four races ago I would have told you that Sebastian is going to DNF (not finish) two times and not score well one time, you would have said that's nearly impossible", said Mercedes team boss Toto Wolff.
"There is also some positives, but for sure now you don't look at the positives because it is not the day to look at them". I tried my all. His teammate Kimi Raikkonen also had vehicle trouble all weekend, but managed to finish fifth after starting down in 11th place.
Alonso enjoyed a run to 11th in the race for McLaren-Honda after starting last due to a power unit penalty, narrowly missing out on a point after falling short in a late battle with Felipe Massa.