Academy, the more physical side and with pace to match, outscored their city rivals 5-3 in tries, four of their touchdowns coming in the opening 20 minutes of the game.
Watson's , however, contributed hugely to what was an entertaining final and deserved huge credit from bouncing back after trailing 24-0 to challenge opponents with effective rugby.
Edinburgh Academy gave indication of their try-scoring capability when centre Jamie Farndale powered down the left wing only to be denied a try by a foot in touch.
But from the next scrum the strong-running Farndale took a reverse pass from stand-off Zander Muir to race in under the posts leaving Grigor Brown with a comparatively simple conversion kick.
Then, when scrum-half and man-of-the-match Alex Glashan made the running from a tap penalty, winger Alex Harris was on hand to take the scoring pass, Brown again converting for a 14-0 lead.
Academy's dominance continued as first their high-scoring wing Freddie Smith used his pace to outflank the Watson's defence for try No3 and then full-back Robbie Orr exploited a gap in midfield to touch down unopposed.
Fortunately for the game, George Watson's recovered from Academy's four-try blitz to open their points account with a try from Ramsay Young, the scrum-half diving on spilled ball behind the Academy line before prop Aodon Donnelly added the conversion.
Donnelly then showed his appetite for tries with Watson's second score, finishing a move triggered by No8 Zach Courtney's drive off the back of a scrum. The prop then applied his kicking technique to convert his own try, cutting the lead to ten points with the scoreline at half-time reading 24-10.
Academy started the second half as they had done in the first period of play with Farndale making a dash to the line, but again the strapping centre was stopped by good cover defence.
But not so the mercurial Smith who used his pace and guile to outsmart the Watson's cover with an astutely judged swerve before touching down in the corner for his side's fifth try.
As they had in the first half, Watson's recovered and hit back with some impressive attacking rugby that ended with lock Matthew Horsman powering over from close range, Andrew McMillan adding the conversion to end the scoring
Scorers: Edinburgh Academy: Tries: Farndale, Harris, Smith (2), Orr. Cons: Brown (2). George Watson's College: Tries: Young, Donnelly, Horsman. Cons: Donnelly (2), McMillan.
Edinburgh Academy: Robbie Orr; Alex Harris, Jamie Farndale, Grigor Brown, Freddie Smith; Zander Muir, Alex Glashan; Tom Mitchell, Angus Lutton, Josh Haining, Justin Brackenridge, Ronan Seydak, Cameron Simpson (capt), Chris Thomson, Chris Dean. Substitutes used: Rory Simpson, Angus Scott, Magnus Skirving, Fergus Greig, Davis Catonio, Jonty Bredin, Jamie Hartop.
George Watson's College: Dominic Johnston; Jack Broadley, Andrew McMillan, Pete Ferguson, Chris MacBeth; Euan McKean, Ramsay Young; Sean Sproule, Adam Freeland, Aodon Donnelly, Matthew Horsman, Rhys Jack, Nick Hurn (capt), Zach Courtney, Ross Blair. Substitutes used: Darren McLuskie, Jamie Gregor, Ross Gregor, James Hassall, Callum Anderson, Giuseppe Pia, Iain Gilmore.
Referee: J Matthew (Edinburgh Society).