The Irish heavyweights, European champions in 2006 and 2008, prevailed through tries in each half from wing Keith Earls and skipper Peter O'Mahony, while Ian Keatley kicked 10 points.
Gloucester, though, delivered a stirring display and they went down fighting, arguably deserving more than Charlie Sharples' converted try as Munster triumphed 20-7.
It means Munster are now through to their 15th Heineken quarter-final - an ongoing tournament record - as they joined fellow qualifiers Ulster, Leicester, Clermont Auvergne and Toulon in the last eight.
And if they beat Thomond Park visitors Edinburgh in next weekend's final pool fixture, then it should be enough to secure a home tie as one of the top four group winners.
Leicester ensured Heineken Cup quarter-final qualification remains in their own hands as they picked up maximum points at Benetton Treviso.
The Premiership champions were made to work hard for a fourth straight win in Pool 5 but they turned a 13-8 half-time deficit into a 34-19 success at the Stadio di Monigo.
A brace of Miles Benjamin tries were accompanied by an early effort from Julian Salvi and a penalty score, with Owen Williams adding a penalty and David Mele kicking three penalties and a conversion to set up a mouth-watering clash with pool leaders Ulster at Welford Road next week.
Matt Berquist contributed 14 points for Treviso, with prop Lorenzo Cittadini claiming their solitary first-half try.
Sitiveni Sivivatu's late try halted Harlequins' Heineken Cup recovery in its tracks as Clermont Auvergne clinched a 16-13 victory at the Stoop.
Clermont fly-half Brock James failed to convert the Kiwi flyer's 72nd-minute score but the Australian landed a late penalty to seal victory for the French giants and end Quins' hopes of reaching the knock-out stages.
Danny Care's moment of magic in the first half had inspired Quins to a 13-3 lead at the break, at that stage sustaining the Londoners' hopes of becoming the first side to lose their first two matches and reach the quarter-finals.
But scores from Napolioni Nalaga, who capitalised on a costly error from England full-back Mike Brown, and Sivivatu sealed Harlequins' fate.
Glasgow Warriors came back from 10-0 down to win at Exeter and climb off the foot of Heineken Cup Pool Two.
The Warriors' 15-10 victory completes a treble over the Chiefs having won the home tie 20-16 in October and achieved a 29-26 pre-season friendly at Sandy Park.
It sets up an interesting final pool tie for against Toulon at Scotstoun for the Warriors, who can still pip Cardiff Blues for second place.
Connacht got the required victory to keep themselves in the hunt for a Heineken Cup quarter-final place, as they ran out 17-point winners over Zebre at the Sportsground.
Matt Healy and Robbie Henshaw scored tries either side of half-time and 20-year-old tournament debutant Jack Carty kicked the rest of the points for Pat Lam's men.
Carty kicked two penalties to Luciano Orquera's lone first-half effort, with winger Healy's first Heineken Cup try - scored while Zebre's Filippo Ferrarini was in the sin-bin - moving Connacht 13-3 ahead at the break.
Henshaw then touched down with the promise of more scores, but the concluding 37 minutes were scoreless as the hosts' bonus-point push failed to materialise.
The result is enough to keep Lam's charges in contention to reach the last eight, a scenario which is only possible if they beat Saracens at Allianz Park next Saturday and other results go their way.
Toulon produced a stunning second-half display to beat Cardiff Blues 43-20 and book their place in the Heineken Cup quarter-finals.
The reigning European champions led by just two points at half-time but powered their way past the forlorn Blues after the break.
Indiscipline cost the Blues dearly as four yellow cards and three penalty tries, combined with a try for wing David Smith, were enough to hand Toulon the win.
Edinburgh preserved their slender hopes of remaining involved in Europe when they posted a home win over Perpignan in Pool 6 of the Heineken Cup.
However, the absence of a four-try bonus point means that even an Amlin Challenge Cup spot is highly unlikely.
The Scottish outfit had tries from Tom Brown, Cornell Du Preez and Dougie Fife plus a 12-point contribution from skipper Greig Laidlaw, while Maxime Delonca touched down for Perpignan and Wales international James Hook - deployed at full-back on this occasion - landed three penalties and a conversion.