Munster, who have not lost a European Cup match at their home ground Thomond Park in Limerick in three years, go on to meet Biarritz after the French side beat Welsh team Ospreys 29-28 in Spain earlier in the day.
Former All Blacks wing Howlett touched down twice and fullback Paul Warwick and centre Jean de Villiers scored a try each for Munster. Fly-half Ronan O'Gara kicked 13 points.
Northampton mounted a spirited challenge in the first half and led 16-13 at halftime. But they collapsed after the interval and had to be content with a try from centre Jon Clarke and 14 points from the boot of flyhalf Stephen Myler.
Tries to wing Takudzwa Ngwenya and fullback Iain Balshaw, 10 points from the boot of scrumhalf Dimitri Yachvili and three drop goals by centre Damien Traille had earlier given Biarritz their narrow victory over Ospreys in an entertaining game.
Opsreys ran in three tries to number eight and captain Ryan Jones, fullback Lee Byrne and substitute wing Nikki Walker, and flyback Daniel Biggar contributed 13 points.
Biarritz opened up a 10-0 lead, with a splendid try from Ngwenya, in San Sebastian, Spain, where the club from the French Basque country often play their European Cup matches.
Ospreys responded and changed ends trailing only by one point at 16-15. The Welsh side fought until the very end, a late try by Walker converted by Biggar putting them one point behind their hosts with four minutes left.
Holders Leinster made the semi-finals with a 29-28 win over French side Clermont on Friday. They will next face Toulouse.