The game was played in a muted atmosphere at Croke Park, with vast sections of the 82,000-seater stadium lying empty and only a few thousand spectators paying to watch the encounter.
Joe Kernan's Ulster side mounted a spirited second-half comeback after trailing by six points early in the contest.
Kernan's Crossmaglen clubmate Jamie Clarke, who opted to play in the interpro decider rather than turn out for Armagh's rescheduled National Football League game against Wexford on Saturday night, netted from the spot to help his side as Ulster recovered from their disastrous start to trail 0-9 to 1-4 at the break.
Dublin's Bernard Brogan was the star performer for Leinster, scoring 11 points including nine frees, but Ulster were the better side in the second half, and Clarke's second goal coupled with a three-pointer from Monaghan's Conor McManus put Ulster into a commanding lead early in the second half,.
Leinster fought back with Brogan landing a succession of frees, but scores from Clarke, Sean Cavanagh and Mark McHugh kept Ulster's noses in front.
Lienster finished strongly and Derry's Chrissy McKaigue was red carded a minute from time, but Ulster held on for the victory.