Co-founder Mike Shinoda told the crowd: "We want to dedicate this award to him, to his memory, to his talent, to his sense of humour, to his joy".
Bennington, who went to high school in the Valley and supported Banner Health's Cardon Children's Medical Center, took his own life in July.
Linkin Park has had a rough year, but last night was supposed to be a celebration.
If you're thinking about suicide or know someone who may need help, the National Suicide Prevention Lifeline is 800-273-8255.
See the One More Light rockers pick up their gong for Favourite Artist in the Alternative Rock category. "And make Chester proud", they said.
Love all! Serena Williams ties the knot
The over one-minute commercial opens with a baby lying on her crib before Williams picks her up and cradles her on her shoulder. The little girl also featured in the photographs of her parents' lavish star-studded wedding in New Orleans on November 16.
The AMAs were a night of ups and downs for Linkin Park.
The band's surprise appearance at the Microsoft Theater in Los Angeles on Sunday for the AMAs marked their first in months.
His colleagues Mike Shinoda, Rob Bourdon and Brad Delson accepted the award after Linkin Park beat out fellow nominees Imagine Dragons and Twenty One Pilots. The album will have some unreleased tracks from their 2017 World Tour.
The singer died by suicide in July and since then, various tributes have been paid to his memory that rang from fans sharing personal stories about what Chester and his music meant to them to Chris Martin covering "Crawling" at a recent Coldplay gig. Chester who is world famous for his emotional songs lost his battle against alcohol and depression.