Ferrari's Kimi Raikkonen was fastest in the third and final practice Saturday for the Malaysian Grand Prix, with championship leader Lewis Hamilton in a Mercedes only fifth.
Vettel was second, 0.162 seconds behind team-mate Raikkonen but was called into the pits four minutes before then of the session with an engine problem.
Daniel Ricciardo in a Red Bull was third on the Sepang International Circuit ahead of Valtteri Bottas in a Mercedes.
Hamilton has a 28-point lead over Vettel in the Formula One drivers' standings ahead of Sunday's race. Qualifying later will determine grid positions.