And Saracens suffered a double blow, with their defeat meaning England will provide just six Heineken Cup representatives next season, compared with seven for France.
Saracens have no realistic chance of securing a top-six Guinness Premiership finish with just two league games remaining, meaning they are consigned to a place in the second-tier European Challenge Cup.
Skipper Neil de Kock said: "The gut-wrenching part is we are going to have to wait another two years to have another crack at the Heineken Cup.
"And that is a really tough pill to swallow."
England's likely Heineken Cup qualifiers are Gloucester, Bath, Wasps, Harlequins, Sale Sharks and Leicester, although Worcester will secure one of the spots if they beat Bath in this season's Challenge Cup final on May 25.
All Saracens can do though, is reflect on what might have been following defeat against a team Gaffney believes will lift the trophy against three-time European champions Toulouse in Cardiff next month.
Former Munster boss Gaffney said: "I know Toulouse can do some wonderful things.
"But I like the hard edge of Munster. They have still got a very good set-piece game, and I also think they are strong enough right across the pitch."
With Gaffney leaving Saracens this summer, planning for next season is already well advanced under the direction of his successor, Australian Eddie Jones.
The former Wallabies head coach is likely to make a number of new signings, although Saracens have already announced the arrivals of Bath and England lock Steve Borthwick, plus former Wales captain Michael Owen from Newport Gwent Dragons.
They have also snapped up Fiji under-19 international Iliesa Keresoni - the younger brother of their explosive wing Kameli Ratuvou - who is joining Saracens' academy next term.
Munster, meanwhile, now switch attention to their fourth Heineken Cup final in nine seasons - although it is debatable whether Toulouse will give them a tougher game than Saracens managed.
Munster rugby director Declan Kidney added: "Our respect for Alan (Gaffney) is so enormous that we knew it could be our final game (in this season's tournament).
"We've scrimped, we've clawed and crawled just to be where we are now, and that is a huge achievement for the players involved.
"It was exactly as we expected. We knew Saracens were a very good team.
"We probably played as well as Saracens allowed. The group I'm working with are hugely self-critical and so they are disappointed at the errors they made.
"But with a team that largely grew up locally, we've managed to reach another final and that is a huge achievement.
"We shouldn't forget that, because these kind of days aren't going to last forever."