Adding to Kelly's hat-trick, his UCD colleague Sam Coghlan-Murray and Clontarf centre Collin O'Shea also touched down, with Dublin University out-half Cathal Marsh chipping in with two penalties and two conversions.
Munster replied with tries from UL Bohemians' JJ Hanrahan and Pres Cork lock Cathal O'Flaherty. Hanrahan, who featured for Ireland U-18 Schools side last season, also kicked eight points.
Leinster were only 8-7 ahead at half-time, Munster making it a one-point game courtesy of a forward rumble which created O'Flaherty's try.
But the hosts had the win within their grasp after Kelly had broken through for his second try and Coghlan-Murray romped over for a superb score from 80 metres out, showing great pace down the left.
Hanrahan, who was in excellent form, replied with a well-taken 73rd minute try, but Leinster had the final say through O'Shea and his centre partner Kelly, the latter try coming after a terrific surge from number 8 Eoin Joyce.
Click here to view photos from the Leinster U-20s v Munster U-20s match.
Sealing a second place finish in the Championship, Ulster battled their way to a 24-19 triumph over Connacht at the Sportsground on Friday.
Banbridge's Chris Leathem opened the scoring in the 16th minute, getting on the end of Blane McIlroy's box kick which Connacht failed to defend. Out-half Paddy Jackson, an Ireland Under-19 international, added the extras from in front of the posts.
Buccaneers clubman Callum Boland booted a penalty in response. Jackson snapped back with a penalty of his own, following good pressure from the Ulster pack, but Ireland U-18 Clubs international Boland landed two more penalties to close the gap to 10-9 for half-time.
Ulster had two players sin-binned in a lively first half, with lock David Whann and scrum half McIlroy seeing yellow.
It was Connacht's turn to lose a player to the sin, 12 minutes into the second half. Creggs' David Butler was adjudged to have taken out Leathem in the air. Crucially, Ulster took full advantage with Hackson and team captain Andy Warwick crossing for quick-fire tries.
A late Connacht onslaught yielded a try for winger Tadhg Leader from Galwegians. Boland's conversion made it a five-point game, however Ulster stood firm to take the spoils.
2010/11 IRFU UNDER-20 INTERPROVINCIAL CHAMPIONSHIP:
Friday, September 3 -
Friday, September 10 -
Friday, September 17 -