Manning's performance gave him 51 scoring strikes for the season, bettering the mark set by New England's Brady in 2007.
Three of his TD tosses came in the fourth quarter. Eric Decker hauled in the first two and Manning hooked up with Julius Thomas on the record-breaker with 4:28 left.
The Broncos (12-3) clinched the AFC West title with the victory.
Manning finished 32-of-51 through the air for 400 yards and no interceptions.
Decker made 10 grabs for 131 yards and Demaryius Thomas hauled down eight passes for 123 yards and caught Peyton's other scoring toss.
Matt Schaub made good on 18-of-37 passes for 176 yards, a TD and two interceptions for the Texans (2-13).