maiden win on the PGA Tour secured a debut in The Open later this month for the 25-year-old.
The overnight leader made eight birdies and a single bogey at TPC Deere Run as he finished on 28 under to seal a commanding victory.
“Qualifying for The Open was just an added incentive to this,” said Thompson.
“The goal was to win the golf tournament after getting off to a great start and I was able to finish it off.”
Chinese Taipei’s CT Pan also claimed a spot in The Open at Royal Troon by finishing joint second on 24 under alongside Michael Thorbjornsen and 20-year-old amateur Luke Clanton.
Pan took the second qualifying place that was available from the John Deere Classic courtesy of his higher position in the world ranking.
England’s Aaron Rai, who was in a share of the lead going into the third round, shot a 69 to finish on 21 under.
Compatriot Harry Hall was one shot further back after a final-round 65.