And with Glasgow Warriors seeing off Connacht even a bonus-point win would not have been enough for Ulster to reach the semi-finals.
Munster's European ambitions were ended in the quarter-final stage by their Northern Irish opponents and they clearly had revenge on their minds at Thomond Park.
And Tony McGahan - who will return to his native Australia in the summer - watched as his side ran in five tries ahead of a RaboDirect PRO12 semi-final away to the Ospreys in Swansea.
However the Munster head coach will be concerned at seeing skipper O'Connell helped from the field early in the second half with what appeared to be a knee injury.
Munster made a flying start to the game as top scorer Simon Zebo went over after just seven minutes. It was the 22-year-old winger's eighth of the RaboDirect PRO12 in his breakthrough season for the province.
Zebo was again in the action five minutes later as Andrew Trimble took him out without the ball, the Ulster winger sent to the bin as a result.
Scott Deasy and Paddy Jackson exchanged penalties with the home side leading 10-3 just before half-time.
However, right on the stroke of half-time Munster's pressure told and Peter O'Mahony forced his way over for the second try, Deasy's conversion making it 17-3 at the break.
Munster continued to dominate after the break and scored their third try when Mike Sherry made the most of a powerful drive from a lineout.
With his final act of the game the hooker flopped over the line with Ulster unable to stop the Munster rolling maul. Deasy converted but Ulster reacted immediately with a fantastic solo try from youngster Iain Henderson.
The versatile back row forward collected the ball from Ian Humphreys on the Munster 22 and showed great pace and power to hold off Felix Jones and Zebo and stretch for his first RaboDirect PRO12 try.
The two sides kept fighting in the second half but Munster had to wait until the 77th minute to seal the bonus point as replacement prop Stephen Archer barged his way to the line, Declan Cusack's conversion making it 31-8.
And in the final minute replacement Tommy O'Donnell showed some good pace as he streaked over to seal the win.
|Munster Rugby Score Card|
|Ulster Rugby Score Card|