Popp, who's scored six goals at the tournament including both of Germany's goals in their semi-final win over France, is understood to have sustained a muscular injury.
The Wolfsburg striker was named in Martina Voss-Tecklenburg's starting line-up but sustained the injury moments before the start of the Wembley clash.
Bayern Munich striker Lea Schuller replaced Popp in the starting XI.
Former England international Lianne Sanderson said on talkSPORT: "I'm in shock. When they put the team announcement on the screen I thought they'd made a mistake.
"That's unfortunate. I feel for her, I really do.
"It does change everything. Mille Bright and Leah Williamson will have to take care of Schuller now."
It's been an open start to the final with Lionesses record goalscorer Ellen White having a header saved by Merle Frohms.
Meanwhile, Lucy Bronze blocked a shot that was heading for Mary Earps' goal in the tenth minute.
The visitors have had the biggest chance of the final so far with Leah Williamson blocking two Marina Hegering efforts from close range in quick succession off the line.
England fans had a few nervous seconds just after that flurry with VAR conducting a potential penalty check after the ball hit Williamson on the hand, however, a spot-kick wasn't awarded.