The Broncos started slowly as they were forced to settle for a 21-yard field goal on their first drive from Brandon McManus.
Colts quarterback Andrew Luck then threw an interception as Rahim Moore picked off the pass following a deflection. Peyton Manning drove his side downfield and found Thomas in the endzone for a three-yard score.
The same combo struck again on the next drive as Manning fired the ball to Thomas on a crossing route and the receiver sprinted into the endzone for the 35-yard touchdown.
Thomas completed his hat-trick just before the break when he was lined up in single coverage against LaRon Landry and Manning found him on a slant route for a five-yard strike.
The Colts hit back just before half time when Luck managed to escape the pocket and run over to the right sideline before leaping towards the pylon to complete a nine-yard touchdown.