Munster’s Champions Cup fate for the knockout rounds was taken out of their hands as they went down at Franklin’s Gardens on Saturday.
Tom Seabrook's team secured top spot in Pool 3 and a top seeding for the knockout stages in their bonus-point victory.
Having lost in their bid to earn top spot in the pool Munster must now wait on the outcome of Sunday’s clash between pool rivals Saracens and Castres, the result impacting Munster’s final position and their opponent's difficulty level in the knockout rounds.
Saints had scored the opening try on 14 minutes. Munster and Saints slugged it out in midfield but Calvin Nash finally broke the game open on 23 minutes, with Jack Crowley scoring the conversion.
He added a penalty soon after and the Irish province added further pressure when Nash scored his second try on 32 minutes. Crowley missed the conversion but Munster were 15-5 ahead as half-time approached.
Northampton went in search of a reply and laid siege to the Munster tryline once more, regularly eking penalties and after a yellow card, Gavin Coombes was sent to the bin on 40 minutes.
Saints struck immediately with a try and conversion ending the first half at 15-12.
As the second half got underway Seabrook grabbed another try.
Coomes' return could not halt Northampton’s momentum, with another try and conversion sending them into a 22-15 lead on 54 minutes.
Crowley closed the gap with a penalty three minutes later, only for Smith to reply and maintain his side’s advantage.
Munster were not unbowed, Diarmuid Kilgallen providing the finish on his competitive debut.
The conversion made it 27-25 but back came Northampton, Seabrook grabbing his hat-trick of tries and Smith’s two points from the tee opening up a 34-25 lead as the game entered the final 10 minutes.
A penalty for offside followed with Munster tapping from five metres out, and then sending the ball out wide to the left for Kilgallen to grab his second of the game, and a try bonus point, with Crowley’s touchline conversion making it a two-point game with a minute remaining.
But it was not to be, Saints throwing numbers into the breakdown and claiming a match-saving turnover with the clock past 80.
Munster will have to wait nervously on Sunday’s Saracens-Castres clash but their two match points could be crucial.