The meeting of the two Dublin teams lived up to the expectations of it being a thrilling derby with four goals scored in the first half - two apiece for Noelle Murray and Aine O'Gorman - before Leanne Kiernan netted the all-important goal.
Shels took the lead on 11 minutes when Murray controlled the ball, looked up and struck a long-range shot that UCD goalkeeper Monica McGuirk simply couldn't get to.
It didn't take long for Eileen Gleeson's side to hit back though as O'Gorman - top scorer in the Continental Tyres Women's National League this season - headed in after connecting with a cross from Jetta Berrill.
There wasn't much between the teams in the opening exchanges and even when Murray got her second goal of the game - through a neat finish inside the penalty area - it didn't rattle UCD.
In fact, UCD were quickly back on level terms as O'Gorman raced on to a through ball to coolly slot the ball past Shels stopper Amanda McQuillan. And it stayed at 2-2 going into the interval.
After the break, Kiernan finally got a reward for her hard work when she broke the offside trap to meet Siobhan Killeen's pass and convert a left-footed shot. That proved to be the winning strike.
Shels can still go on to become double champions should they conquer Wexford Youths WFC in the Continental Tyres Women's National League Play-Off on Sunday, May 22 at Tallaght Stadium.
Shelbourne Ladies: McQuillan; Keenan, Slattery, Walsh, Beirne; Graham, Creagh, Murray; Watters, Kiernan, Killeen.
UCD Waves: McGuirk; Berrill, Hackett, Cahill, Prior; Russell, Mustaki, Duggan, Ryan-Doyle (Grant 69); Nolan, O'Gorman.
Referee: Deirdre Nolan.