Starved of territory for long stretches of a pedestrian first period, a late push yielded a penalty try for Munster who went to the break 10-3 in front.
The gap was out to 14 points when Simon Zebo split the defence five minutes after the break, and Peter O'Mahony soon crashed over for the third try.
But Munster were unable to fashion a fourth for the bonus point, and Ulster gained a late consolation score when replacement Ali Birch finished off a fine three-man move.
Leinster cruised to an easy 17-0 win over Connacht in the day's other all-Irish clash.
Ian Madigan converted his own try after 33 minutes to score the only points of the first half, then added a penalty and a conversion of Jack McGrath's try late on to finish off the victory.
Tries from Edoardo Gori and Leonardo Ghiraldini set Treviso on their way to another victory over Zebre as they won the Italian derby 26-18 in the RaboDirect PRO12.
Gori and Ghiraldini scored either side of half-time while Kris Burton collected 16 points with the boot, kicking two drop-goals, two penalties and two conversions.
Zebre scored late tries through Paolo Buso and Giovanbattista Venditti but it was not enough for them to claim a bonus point.
Glasgow Warriors claimed the 1872 Cup for a fourth successive season as Edinburgh's response came too late in a 21-17 defeat at Murrayfield.
The 1872 Cup is awarded to the aggregate winners of the derby double header and the Warriors won the first contest 23-14 at Scotstoun following a fast start - before repeating the first-half onslaught in the capital.
Glasgow had nine fingers on the trophy and the RaboDirect PRO12 points almost sewn up after 40 minutes, taking a 16-3 lead courtesy of tries from New Zealand-born, Scottish-qualified wing Sean Maitland and Ruaridh Jackson, plus two penalties from Peter Horne, who was also sin-binned.
A Greig Laidlaw penalty was the solitary reply for Edinburgh, who last won the 1872 Cup in 2008-09, and their hopes were hit further when Allan Jacobsen was sin-binned and Henry Pyrgos scored a try.
Roddy Grant's converted score after 59 minutes gave the hosts some hope and Tim Visser scored five minutes from time, with Laidlaw kicking his side within four points.
But the late rally ended there as Glasgow saw out the remaining seconds to retain the derby bragging rights they have held since the 2009-10 season.