The Bulgarian international enjoyed a fine season before being diagnosed with the illness last month and he is currently undergoing treatment.
Petrov did not attend the awards ceremony at Villa Park on Monday night, but said in a video message: "Sorry I can't be with you but I've got a little issue I need to fight. I hope you haven't given me this award because of my situation. I thought I had a quite okay season!"
The midfielder added: "But I think we all deserve this award because we've worked so hard this season."
Fellow midfielder Stephen Ireland was voted the supporters' player of the year after finally showing the form which led to Villa signing him from Manchester City two years ago.
Ireland had been loaned out to Newcastle last season after failing to impress the then manager Gerard Houllier but he has enjoyed more first team involvement under current boss Alex McLeish.
Rookie striker Andreas Weimann, who scored vital goals against Fulham and Stoke, was named young player of the year.