Shipley, the younger brother of Texas career receptions leader Jordan Shipley, put the Longhorns ahead 20-9 in the third on a pass from wide receiver John Harris.
Garrett Gilbert passed for 239 yards, with 115 going to Mike Davis in Texas' new offense under first-year coordinator Bryan Harsin. Coach Mack Brown overhauled his staff after the Longhorns went 5-7 and missed a bowl in 2010, Texas' first losing season since 1997.
Chris Boswell kicked three field goals for Rice, which has lost 40 of the last 41 meetings with Texas.
The win unveiled some new wrinkles in the Texas offense with some new and old names and faces. It was clunky at times, efficient at others.
Most important for the Longhorns was getting the win at home, where they were 2-5 in 2010.
Texas fans who last watched Jordan Shipley rip through defenses in 2009, heard Jaxon's name mentioned as one of the brightest stars of training camp. He didn't disappoint, wrestling the ball away from a defensive back for a touchdown that helped the Longhorns break open a close game.
The score came on a reverse pass where backup quarterback David Ash handed off to Whittaker, who tossed the ball to Harris to find Shipley in the end zone. Shipley took the ball away from Rice safety Paul Porras at the goal line.
Gilbert, scorned by many Texas fans after throwing 17 interceptions last season, did not have a turnover and showed a deft touch on his deep passes and his 26-yard fourth-quarter TD pass to Whittaker.
The Longhorns also unveiled a new wildcat formation that kept the Owls off guard near the end zone, and a tougher running game that was able to grind out 229 yards. Freshman tailback Malcolm Brown came on late and finished with a game-high 86 yards on 16 carries.
The defense, under new coordinator Manny Diaz, was solid, giving up 224 yards and keeping the Owls out of the end zone.
Then again, all of that came against Rice, a team that Texas routinely lines up for an early-season pounding.
The Longhorns offense showed it still has a way to go. Penalties, sacks and early problems finishing drives with touchdowns made it clear the transition to Harsin after 13 seasons under former coordinator Greg Davis will take some time getting used to.
Rice kept the game close through most of three quarters on the leg of Boswell, who booted field goals of 42, 49 and 26 yards. His last pulled the Owls within 13-9 before Texas finally created some breathing room with Shipley's touchdown.
Tyler Smith led Rice with 67 yards on 10 carries.
Gilbert, who had to win a four-way battle to keep his starting job in training camp, was solid if not spectacular against the Owls. He connected with Davis for completions of 56 and 53 yards. The first set up a first-half field goal. The second came during a 99-yard drive that Whittaker finished with a 7-yard TD run for a 27-9 Texas lead. Gilbert also scrambled 22 yards early in the game to set up another field goal.
Rice sacked Gilbert twice in a row on the first drive of the third, drawing a smattering of boos from the home crowd of 101,000 that was still waiting to see Texas crank up a well-oiled offensive machine.
Texas responded with a 72-yard drive for its second touchdown on the pass from Harris to Shipley.