Tyrone's Peter Harte scored a penalty to add to his eight points in a classy individual display.
Pete McGrath's Ulster side scored earlier goals through Aidan Breen and Enda Lynn.
In the hurling semi-final, Munster saw off Ulster 3-21 to 0-15 in Thurles.
Once again, the competition failed to capture the public's interest with crowds of around 100 attending the games at Parnell Park at Thurles while similar paltry amounts of spectators watched Saturday's two other semi-finals.
Munster got off to a strong start in the football semi-final and led by 0-5 to 0-2 after 16 minutes, with Waterford's Paul Whyte firing three early points, and Kerry's Tommy Walsh and Clare's Gary Brennan also on target.
However, Ulster launched a strong comeback firing 2-7 without reply, including goals from Breen and Lynn in the 18th and 30th minutes respectively.
Munster lost their captain Aidan O'Mahony to a black card in the 27th minute.
Whyte's fourth point arrived in injury-time, for Munster's first score in 16 minutes, as Ulster led by 2-9 to 0-6 at the break.
Munster responded well in the second half, outscoring their opponents by 1-3 to 0-1 inside seven minutes of the restart, with Clare's Jamie Malone netting their goal.
However, Ulster always kept on top with Harte excellent from play and frees, while Armagh's Stefan Campbell also contributed strongly with five points from play.
Ulster will face Connacht in the final next weekend.
Munster booked a hurling final date with Leinster following the win over Ulster before 62 spectators at Semple Stadium.
All-Ireland final man-of-the-match Seamus Callanan starred with 1-7, claiming Munster's second goal in the 40th minute.
The hosts were always on top in this game, and led by 1-10 to 0-7 at half-time, with Mikey Breen netting their first goal.
Armagh's Conor Corvan (0-3) kept Ulster in touch, with three of their seven first half scores and Antrim's Ciaran Clarke (0-7) also performed strongly.
However, once Callanan netted Munster's second goal, this put the game beyond the Ulstermen, with Stephen Bennett netting the final goal late on.
Ulster will meet holders Connacht in the Interprovincial football decider after Sunday's eight-point semi-final win over Munster at Parnell Park.