Backup quarterback Blake Bell scored on a 55-yard keeper in the fourth quarter for the longest run by a quarterback in the Stoops era.
Lache Seastrunk ran for 91 yards and three touchdowns for Baylor (4-5-, 1-5 Big 12), the last score getting the Bears within eight with 1:26 to play after quarterback Nick Florence got in on the 2-point conversion.
LaColtan Bester recovered the ensuing onside kick, sealing the win for Oklahoma (7-2, 5-1).
Stoops moved past Bud Wilkinson with his 146th victory. He's 11 wins shy of Barry Switzer's school record of 157.
The Sooners never fully shook free of the Bears, who had lost four in a row prior to last week's win against last-place Kansas.
Bell provided some breathing room with his big run out of the "Belldozer" short-yardage package -- the longest for an Oklahoma quarterback since Patrick Fletcher in 1998 -- that made it 42-26 with 14:14 remaining.
The Bears, who entered the game with the nation's top overall offense and top passing attack, piled up 252 yards on the ground and became the fourth Sooners opponent to surpass 200 yards rushing. Florence had 83 yards and a score, to go with 172 yards on 12-for-33 passing with no interceptions, and Glasco Martin ran for 60 yards.
Baylor had a chance to tie it midway through the third quarter, after Seastrunk stretched the ball over the goal line on a 2-yard touchdown run to make it 28-26. But the Sooners snuffed out Jarred Salubi's try for the tying 2-point conversion on an option pitch from Levi Norwood, who got the ball on a jet sweep handoff from Florence.
Jones then led Oklahoma on a 12-play, 75-yard drive that Damien Williams finished off with a 17-yard touchdown run right up the middle. The Sooners' defense stiffened after that, forcing a three-and-out that set up Bell's insurance run.
Oklahoma won for the 21st time in 22 meetings in the series -- with the only loss coming last year when eventual Heisman Trophy winner Robert Griffin III led the Bears to a 45-38 victory at home while amassing the most yards ever by a Sooners opponent (616).
Oklahoma's defense was up to the task better this time. Terrance Williams, the nation's top receiver, had six catches for 91 yards -- but that was 76 below his average. Florence also had a season low in passing yardage, getting held to 127 yards fewer than any other game this season.
The usually quick-striking Bears -- who average 110 seconds on their typical scoring drive this season -- seemed to be getting back in the game when they put together a methodical, 17-play drive to move within 21-17 on Seastrunk's 4-yard touchdown run with just 32 seconds left in the first half.
Baylor was set to get the ball first in the second half, possibly with a chance to go ahead. But even that little time left room for Oklahoma to take advantage of the nation's worst defense.
Brennan Clay picked up dribbling kick and returned it 39 yards into Baylor territory, and the Sooners needed just two plays to take advantage with Jones finding a diving Justin Brown in the end zone for a 35-yard scoring strike and a 28-17 halftime edge.