Rossi was sidelined after suffering fractures to his right leg in a training crash and missed his home Grand Prix at Misano last weekend, with Yamaha opting not to field a replacement.
However, the manufacturer is obliged to enter two riders at MotorLand Aragon, and has settled on Dutchman van der Mark to partner Maverick Vinales.
Van der Mark, 24, competes in the WSBK with Yamaha, having switched from Honda for 2017, and currently holds seventh in this year's standings.
"I'm excited to be given the opportunity to ride the YZR-M1 at the Aragon MotoGP round," said van der Mark.
"I've never ridden a MotoGP bike before, so this will be a completely new experience for me. I'm very curious to see what it feels like to ride on such a machine.
"I realize that it won't be easy going straight into an official practice session without any prior testing. Nevertheless, I'm very grateful to Yamaha for the opportunity.
"I'm sure it will be a great learning experience."
Yamaha Managing Director Lin Jarvis added: "Having previously used Katsuyuki Nakasuga to fill in for Jorge Lorenzo in 2011 and Alex Lowes to replace Bradley Smith [at Tech 3] in 2016, we decided that Michael van der Mark should have the opportunity this time around.
"It is never easy to step in to replace another rider and even more difficult to replace Valentino Rossi, but we believe that Michael has all the credentials and experience to do a good job.
"We will give him our very best support and wish him every success for this exciting opportunity."
Yamaha also noted that Rossi is making "good progress" in his recovery.
09/09/17 Yamaha MotoGP team boss Lin Jarvis has named four riders that could replace the injured Valentino Rossi for the next round of the series at Aragon.
He named its pair of World Superbike riders, Alex Lowes – who replaced an injured Bradley Smith at Tech 3 Yamaha last year for two races – and Michael van der Mark, and Japanese test riders Katsuyuki Nakasuga and Kohta Nozane.
“We have four candidates who could replace [Rossi]," said Jarvis. “Two test riders in Japan, Nakasuga and Nozane, and we have two Superbike riders, Alex and Michael. It will be one of those four."