A good performance by the men in red but it was not enough to start their 2013 campaign with a win.
Munster were leading 14-7 with six minutes remaining when a mistake allowed Ulster in for a second try which was converted to tie up the scores.
Deep in injury time Ulster were awarded a penalty when Munster were penalised at the scrum in what looked like a controversial call allowing Ulster to kick the points to take the lead.
Darragh Moloney and David Johnston were Munster's try scorers and Shane Airey converted both.
Ulster: Rob Haldane (Malone); David Busby (Queens University Belfast), Ross Adair (Ballynahinch), Mark Best (Belfast Harlequins), Jacob Knight (Irish Exiles); Josh Bingham (Methodist College Belfast), Conor Young (Durham University); Jonny Craig (Queens University Belfast), Michael Lagan (Methodist College Belfast), James Leary (Newcastle University); Michael Campbell (Queens University), Scott Barr (Brighton University); Frankie Taggart (Irish Exiles/Belfast Harlequins) Capt., Josh Atkinson (Instonians), Lorcan Dow (Irish Exiles/Queens University Belfast).
Replacements: Patrick Finlay (Trinity College Dublin), Darryl Morton City of Armagh), Ross Kane (Malone), Alex Thompson (Methodist College Belfast), Ben Alexander (Malone), Michael Rainey (Malone), Paddy Colhoun (Queens University Belfast), Conor McKee (Methodist College Belfast).
Munster: David Johnston (UL Bohemian), Alex Wootton (Exiles), Dan Goggin (Young Munster), Ned Hodson (UCC), Adrian Enright (UL Bohemian), Shane Airey (UL Bohemian), Ryan Foley (Cork Constitution); Mike Lynch (St Senans/UL Bohemian), Max Abbott (Cork Constitution), Rory Burke (Cork Constitution), Patrick Kearns (Shannon), Darragh Moloney (Cork Constitution), Lee Nicholas (Shannon), Aidan Butler (Shannon), Jack O'Donoughue (UL Bohemian) Capt.
Replacements: Ben Burns (UCC), Sean McGee (Shannon), James Maxwell (Cashel), Tadgh Arrigan (UCC), Sonny Dwyer (Cork Constitution), Aaron Atkinson (UCC), Gearoid Lyons (Shannon), Sam Sterling (UL Bohemian)
Munster's U20s Interprovincial Fixtures:
Fri. 13th Sept. Munster U20 v Leinster U20, Thomond Park, ko 7.30pm
Fri. 20th Sept. Connacht U20 v Munster U20, Sportsground, ko 3pm