The Eifel Grand Prix - which sees the Nurburgring return to the calendar for the first time since 2013 - will have Bottas starting at the front after he ended Hamilton's run of five straight pole positions.
In Qualifying 1, Verstappen topped the session with a lap of 1m26.319s, 0.254s ahead of Bottas.
Charles Leclerc will start fourth for Ferrari after a superb qualifying effort, matching his best Saturday performance of the season so far. It was especially hard for teams to get the most grip from their tires in chilly conditions in western Germany. "Record or not, I am approaching this weekend as any other because once you're in the auto, it's pretty much the same", said Alfa Romeo driver Raikkonen, 2007 world champion with Ferrari.
"We're all in the same boat".
World championship leader Lewis Hamilton said on Thursday that Mercedes would need to work hard this week in incorporating the new staff to ensure there was not too much disruption.
Hamilton will have to overtake his teammate on Sunday if he's to match Michael Schumacher's record of 91 wins in F1.
Bottas is hoping to carry the momentum of his victory in Russian Federation two weeks ago into the race and to revive his title bid.
Hamilton has always gone well in the wet, however, and Mercedes have been on another level to the rest this season with eight wins from 10 races and every pole.
President Trump Surprises Supporters Gathered Outside Hospital With SUV Drive-By
Meanwhile, a number of Trump's associates at the White House and with the campaign have also tested positive for the coronavirus. This means they are expected to continue to work - while taking precautions - until a medical recommendation otherwise is given.
Disappointment for Nico Hulkenberg, who finishes last, but given he didn't have any practice whatsoever at the Nurburgring today or yesterday, it's no slant against the German's abilities.
After both Friday sessions were cancelled due to fog and rain that prevented the use of the circuit medical helicopter, there was relief when on-track action began albeit with the notable absence of Racing Point's Lance Stroll, due to an unspecified illness.
He was in the nearby city of Cologne and joked it was like "a heart attack" when he got a call from the team.
"The last lap in Q3 was spot on, just what I was needed. I don't have the details of why, but it's not something I personally support".
The 31-year-old managed three purple sectors on the last lap to stun Hamilton and send a message that the championship battle is far from over yet.
Racing Point's Mexican Sergio Perez, who missed two races in August, remains the only driver so far to have tested positive for the virus.
The last victor of an F1 race at the Nürburgring was Sebastian Vettel driving for Red Bull in the 2013 German Grand Prix.