Series leader Toprak Razgatlioglu had won the previous 13 races in the championship, a record sequence, but is unable to compete this weekend after being involved in a heavy spill during practice on Friday.
He was treated at the medical centre, where he was diagnosed with a back contusion and was subsequently declared unfit to race after undergoing hospital checks.
Van der Mark’s margin of victory at the front was 8.3 seconds, with Ducati-mounted Bautista having a further 16 seconds to spare over Petrucci at the chequered flag.
England’s Scott Redding finished fourth, ahead of Andrea Iannone and Xavi Vierge as several other riders fell off on the soaked track.
Razgatlioglu leads the standings on 365 points, followed by Bulega on 273, Bautista on 243 and Lowes with 213.
Rea remains 10th overall with 86 points and just one podium finish to show for his efforts so far this season, that coming in the Superpole race in the UK round at Donington in July.
The latest Superpole race will be staged on Sunday at 10:00 BST, followed by the second feature race at 14:30.
Four further rounds will be held over six weeks to bring the 2024 championship to a conclusion.