Reigning champion and overall leader Jorge Lorenzo was second fastest on a Yamaha, nearly half a second slower.
Marquez's team mate Dani Pedrosa was third, taking his highest grid position this year on a sunny afternoon with temperatures of around 25 degrees Celsius. Hector Barbera was fourth on a Ducati.
Yamaha's Italian Valentino Rossi will start fifth, the lone non-Spaniard in the top six.
Lorenzo leads Marquez by 10 points in the standings and is chasing his third win in a row on Sunday.
The circuit layout was shortened after Salom's accident, with riders now using the version used at the Spanish Formula One Grand Prix that misses out the high-speed turn 12 where Salom fell.
Salom's death has cast a pall over the seventh race weekend of the season, with a sombre atmosphere as riders took to the track for an extended final practice and qualifying.
Ten MotoGP riders, including Marquez, attended a meeting of the sport's safety commission on Friday and said they would not continue without changes to the track.
"We could not continue exactly the same," said Carmelo Ezpeleta, chief executive of MotoGP promoters Dorna. "If it happened once, it could happen again even if the possibilities were small."
(Reporting by Alan Baldwin, editing by Ed Osmond)
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