More from Maximilian Gunther
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Starting from pole, Gunther took a lights-to-flag win despite early-race pressure from teammate Stroll.
The poleman eventually pulled away from the Canadian, who took his 11th top-two finish in the past five rounds.
Red Bull's Niko Kari kept up with the duo and was only half a second behind Stroll at one point, but eventually settled for third.
Callum Ilott was fourth, a fair bit behind Kari, with Nick Cassidy and Joel Eriksson finishing fifth and sixth respectively.
George Russell was seventh ahead of Sergio Sette Camara and Anthoine Hubert, who lost his race-long rival Ralf Aron late in the race after the Estonian was hit by Harrison Newey at Turn 1.
Ben Barnicoat claimed the final points-scoring position.
With two wins and a second place, Stroll extended his championship to 68 points over the weekend.
He needs to gain seven points on Gunther at Imola to claim the title with a round to spare.
Nurburgring F3: Stroll passes Gunther for Race 2 win
Stroll aiming to seal F3 title in Imola