With the clock already in the red at the Stade Aime Giral, Hanrahan produced a stunning sidestep 25 metres out and touched down out wide to hand the 2006 and 2008 champions their third win in four pool games.
Italian international Tommaso Benvenuti looked to have dealt Munster's hopes of a third Heineken Cup crown a heavy blow when he crossed with less than two minutes remaining but Rob Penney's men kept the ball alive from the restart, with Denis Hurley and Tommy O'Donnell setting up Hanrahan's heroics.
Munster began brightly and thought they had claimed the opening try with just six minutes on the clock when openside flanker Sean Dougall scampered over from 10 metres out.
The celebrations were short-lived, however, as referee JP Doyle called for assistance and the TMO ruled that James Downey was guilty of obstruction.
Instead, it was Perpignan who scored first just moments later through a well-struck penalty from former Scotland U20 fly-half Tommy Allan.
Both sides found themselves down to 14 men after 13 minutes when Munster skipper Peter O'Mahony and Perpignan hooker Romain Terrain were sin-binned for an off-the-ball altercation that led to a mass brawl.
Ian Keatley kicked Munster level after a quarter of an hour but Allan edged Perpignan back in front with his second three minutes later.
His third strike after 24 minutes pushed Perpignan six points clear and it stayed that way until the break, although both kickers should have added to their tally.
Keatley failed from the tee after half an hour and Allan followed suit four minutes later, with Keatley missing again with the final play of the half.
Munster started the second half in a similar manner to the first, as Paul O'Connell and his team-mates repeatedly demolished the Perpignan scrum.
Doyle awarded three penalties and a free kick at a five-metre set piece before finally losing patience and pointing to the posts for a penalty try. Keatley's simple conversion handed Munster the lead for the first time on 50 minutes.
Perpignan responded well and should have gone back in front before the hour. Allen was off target again before they turned down another kickable penalty in favour of a quick tap and the chance went begging when former England number eight Luke Narraway failed to hang on to a dreadful pass out wide.
Perpignan did regain the advantage when Allan struck his fourth penalty from wide on the left after 63 minutes but the lead was short-lived as Keatley made it 13-12 with 13 minutes left.
Benvenuti's try out wide should have been enough for Perpignan but Munster have proved time and time again that they can never be written off in Europe.
- Sports & Recreation
- Tommaso Benvenuti