Romo totaled 341 yards, completing 23-of-39 throws in the third win in four games for Dallas (7-4)
Owens caught seven passes, one of them on a 75-yard touchdown play.
Shaun Hill completed 21-of-33 passes for 303 yards and two touchdowns for the 49ers (3-8), who have lost seven of their last eight games.
Isaac Bruce and DeShaun Foster had touchdown catches for San Francisco.
The 49ers managed only 26 yards rushing, all by Frank Gore.