The music mogul said missing out would make the singer stronger and stop success going to her head.
Lewis was nominated for Best British Album, British Female Solo Artist, British Single and British Breakthrough Act at last month's ceremony, but failed to walk away with a gong.
Cowell is quoted by WENN as saying: "I was glad Leona didn't win at the Brits. It was the best thing that could have happened.
"She's had a lot of things going her way so it shows her that things can be unfair at times. She had the biggest selling [UK] single of last year so it's a mockery that she never won a Brit. This knockback will make her stronger."
Lewis is to debut her new double A-side single during next week's semi-final of Dancing On Ice.