The 35-15 win secured Munster's place in Europe's leading competition along with Leinster, Connacht and Ulster.
With seven places reserved for the Pro12 that means the other competing nations only have once team each.
Glasgow will represent Scotland, Scarlets are Wales' representatives and Zebre take the Italian place.
With only teams in the top six guaranteed a place, two-time European champions Munster were in danger of missing out after dropping to seventh in the table last month.
However, their two closing bonus-point wins over Edinburgh and the Scarlets enabled them to avoid the indignity of failing to qualify for Europe's top-tier club competition for the first time.
"It's very important for us to be in Europe next season," said Munster coach Anthony Foley.
"We still have ambitions of winning trophies again and making sure we're in knock-out stages so it's important for this group to make sure they are playing at the highest level possible."
While Munster's European blushes were spared, they missed out on the Pro12 play-offs as Connacht, traditionally the weakest of the four Irish provinces, confirmed their home semi-final by beating Glasgow 14-7 in Galway.
Pat Lam's Connacht side will have to do battle again with Gregor Townsend's defending Pro12 champions in the semi-final at the same venue on 21 May.
Ulster's 46-26 win over the Ospreys at the Liberty Stadium means Les Kiss' side will face Leinster in an Irish derby in the opening semi-final at the RDS on 20 May.
Ireland's northern province have not won the title since 2005-06 while the last of Leinster's four triumphs came in 2013-14.
With the Ospreys finishing eighth in the table, they miss out on a place in the top-tier European competition for the first time.
Zebre clinched their Champions Cup spot as they leapfrogged compatriots Treviso to move off the bottom of the Pro12 table by hammering the Dragons 47-22 in Italy.
Munster's Pro12 win over the Scarlets at Thomond Park on Saturday ensured all four Irish provinces will compete in next season's European Champions Cup.