The Finn carded six birdies in a faultless round at the London Golf Club to beat Stenson 3 and 1 in the final with one hole to play, giving him his second win of the season.
After both players had won their semi-finals earlier in the day, it was Stenson, who got the better of George Coetzee on the final hole to reach the final, who started the brighter against Ilonen, taking an early lead after the fourth hole.
Stenson's birdie two put him a shot ahead, but Ilonen immediately pegged him back with a par at the fifth, while the Swede could only register a bogey.
By the turn, Ilonen, who beat Joost Luiten 2 and 1 in his semi-final, was one shot ahead thanks to a birdie at the eighth, as Stenson found the water hazard with his tee shot.
The Swede was three behind with four to play, but immediately gave himself a chance with a birdie at 15.
Having halved the 16th, Ilonen only needed to do the same at the 17th to claim the title, but he produced a perfectly judged chip to leave him just past the hole and in prime position for a birdie.
He duly knocked the putt in, but Stenson was unable to do likewise, conceding the hole and handing the title to the 34-year-old.
Meanwhile, Luiten and Coetzee produced an intriguing third-place play-off as both men let two-shot leads slip away to leave the match all square with five to play.
The duo halved all five remaining holes to take it to a play-off, where Luiten produced the goods under pressure.