The German set a best time of one minute 16.170 seconds, 0.059 quicker than Mercedes' Valtteri Bottas who spun at the chicane and hit the barrier, in a hot afternoon session ahead of qualifying.
Vettel, who had also been fastest on Friday, reported some debris in his car at one point.
"Something flew into my cockpit, no clue what it is," said the four times champion.
Ferrari's Kimi Raikkonen was third fastest with championship leader Lewis Hamilton, who is 17 points clear of Vettel after 11 of the 21 races, fourth for Mercedes and 0.579 off Vettel's pace.
"I just don't have that grip," Hamilton, who also spun, said over the team radio in response to being told Vettel's fastest time.
The Red Bull pairing of Daniel Ricciardo and Max Verstappen, who are expected to go well at the Hungaroring, were fifth and sixth respectively with the Dutch 20-year-old complaining of battery problems.
(Reporting by Alan Baldwin, editing by Toby Davis)
