Vettel went into the race at the Autodromo Hermanos Rodriguez knowing he needed to win and hope Hamilton finished lower than fifth to keep his slim title chances alive.
However, despite starting from pole the German saw his hopes evaporate on the first lap of the race when he tangled first with Max Verstappen and then with Hamilton, damaging his front wing and dropping to the rear of the field.
A valiant drive through to fourth place followed, but Vettel admitted he could take little solace in his performance.
“It’s disappointing, obviously,” he said. “It’s not that important what we have done today, it’s more important what Lewis has done.
“He’s done a superb job all year round and deserves to win the title. So congratulations to him. It’s not about anyone else today, it’s about him. It’s his day.”
Vettel’s clash with Hamilton was the latest in a number of on-track confrontations between the two drivers this season, which the German said he had relished.
“I don’t fear him. I like racing with him, but I would have liked a little bit more of that this season. But overall they [Mercedes] were the better bunch.”
Having led the world title heading into the summer break, Vettel’s run at the title was severely dented by retirements in Singapore and Japan and engine problems that forced him to the back of the grid in Malaysia.
Asked if he had any regrets about how the season had panned out, Vettel said simply: “What does it matter now?”