In a postponed qualifying session at Suzuka that took place only hours before the start of the race, Ferrari locked out the front row for the third time this season.
However, Vettel moved off the line early before the lights went out at the start of the grand prix, which hurt his momentum and allowed Valtteri Bottas to swoop into the lead before going on to take the race win.
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Binotto admits that he isn't sure if Ferrari would have been able to keep Mercedes behind if it had a clean start and remained in the lead after the first lap.
"It’s difficult to say," he said. "Certainly, they’ve got better pace than us today in the race, not in quali. It’s true as well that Seb was ahead of Hamilton on the first lap and remained ahead at the end of the race.
"So I think even if you’ve got good pace, it’s always difficult to overtake. If you are one-two at the start, it is difficult to overtake two cars rather than one. But I don’t think that is something which is important, honestly.
"We need to review what was wrong, why we eventually did some mistakes and certainly why the pace wasn’t good enough. In the end, we need to be the best as well in pace."
Mercedes also wrapped up the constructors' title on Sunday, claiming its sixth consecutive championship triumph.
Bahrain International Circuit - Winter testing