Kyle Larson and Martin Truex Jr. led the field to the green flag in Sunday's 110-lapper at Sonoma Raceway.
The first lap went incident-free with Larson holding the lead over Truex and Chase Elliott.
On Lap 3, Truex was able to pass Larson for the lead down into the Turn 11 hairpin under braking.
Allmendinger was charging early, moving from fifth up to second in the first five laps before setting his sights on Truex. But instead he fell back into the clutches of Kevin Harvick, who he waved by without a fight.
In the closing laps of the stage, Truex opted to give up the stage win in order to better set himself up for the finish, pitting with three laps to go. Harvick followed suit and exited the pits just ahead of Truex, but the reigning series champion swiftly took the position back.
Several other drivers also pitted before pit road was closed, including the stage’s biggest mover in Clint Bowyer and the Busch brothers.
Allmendinger stayed out and inherited the Stage 1 win, while Truex was scored back in 11th when the green and white checkered flag waved.
Brad Keselowski was second, Jimmie Johnson third, Elliott fourth and Larson fifth. Ryan Newman, Aric Almirola, Daniel Suarez, Chris Buescher and Kasey Kahne rounded out the top-ten.
There were no cautions during the opening stage, despite Cody Ware stalling in Turn 7 at the end of the stage.
Allmendinger and the rest of the those who stayed out pitted during the break between stages, putting Truex and Harvick back out front.
"Definitely, (Harvick) and (Truex) have better longer run speed," admitted Allmendinger during the break.