First-half tries from Anthony Horgan and Denis Leamy proved the difference as Harlequins battled back in the second half to threaten a surprise in Limerick.
Harlequins were desperate to use the Heineken Cup as a launch pad for their season and took an early lead through the boot of out-half Jeremy Staunton after a promising opening ten minutes. But it was not to last long.
When Ronan O Gara and Rob Henderson combined in midfield, George Harder came in off his wing to pick off the interception only for the pass to glide over his head and leave a clear path for Horgan to glide over the line on 13 minutes.
Worse was soon to come for Harlequins when Staunton, playing against his former team, was sin binned for knocking down what looked a certain scoring pass just yards off his own line. While he was off, his team fell further behind.
Munster wheeled around an innocuous looking scrum, Jim Williams picked up and surged forward before flicking a pass for flanker Leamy to score. Ronan O Gara converted from the touchline and added a penalty for a 15-3 half-time lead.
Staunton pegged Harlequins back with an early penalty after the break but it was a rare score in a nail-biting second half that even saw Harlequins survive a ten-minute reduction to 14 men when replacement hooker Ace Tiatia was yellow carded for a high tackle on Horgan.
Jeremy Staunton slotted over another penalty towards the finish and the Quins persisted but a try was to prove elusive for the visitors.
Final Score: Munster 15-9 Harlequins
Munster (15) 15 Tries: Horgan, Leamy Pens: O'Gara Cons: O'Gara Harlequins (3) 9 Pens: Staunton 3
Munster: Cullen, Lawlor, Kelly, Henderson, Horgan, O'Gara, Stringer, M. Horan, F. Sheahan, J. Hayes, T. Hogan, O'Connell, Williams, Leamy, Foley. Replacements: Flannery, McIlwham, Bowman, Quinlan, Wallace, Prendergast, Burke.
Harlequins: Duffy, Harder, Greenwood, James, Keogh, Staunton, So'oialo, Jones, Fuga, Fitzgerald, Winters, Miall, Easter, Vos, Diprose. Replacements: Tiatia, Worsley, Palepoi, Sherriff, Dunne, Deane, Williams.
Man of the Match: Anthony Foley