Tries from full-back Conor Quinn, Croke and Vasily Artemiev, the Leinster Academy's Russian-born winger, saw the students streak ahead.
Quinn's 15th-minute opener was a thing of beauty as the ball was worked through twelve pairs of hands before the former Munster Under-19 player slid over for Fergus McFadden to convert.
The home side, beaten 31-15 by Shannon in the league last week, gobbled up any turnovers on offer and their excellent ball retention skills meant an upset was very much on the cards.
Croke's try was a case in point as Quinlan was caught in possession in the lead-up to it. Indeed, UCD's performance was all the more noteworthy given the fact that their first choice half-backs - Ian Keatley and Paul O'Donohue - were missing, given their involvement with the Irish Under-20s on Friday night.
But unfortunately the students lost their way in the early part of the second half as they had Matt Nagle (45 minutes) and Killian Lett (60) yellow carded and Shannon capitalised, as only they can do.
Limerick Gaelic footballer Stephen Kelly scored a peach of a try in the 50th-minute as, in a move created by Munster's Mossie Lawlor, he timed his run on the right flank to perfection. He succeeded in collecting Lawlor's lobbed kick forward, at lightning speed, to cross for his sixth try of the season.
Andrew Thompson's conversion cut the gap to 21-17 and Shannon dominated the closing stages with number 8 David Quinlan, who also touched down in the first half, ending a 35-metre sprint with his second try and pacy hooker Sean Cronin weaving through the gaps for a deserved score, as UCD's challenge wilted.
UCD: C Quinn; V Artemiev, F McFadden, N Kearns, K Lett; M Hastings, B O' Neill; JA Lee, G Telford, B McGovern, A Houlihan, R Mandeno, M Nagle, K Croke, K Sheahan.
Replacements used: C Doyle for Houlihan, E O'Malley for Kearns, B Hall for McGovern, M Buckley for O'Neill, L McIerney for Telford.
Shannon: M Lawlor; S Kelly, P O'Connor, J Clogan, D O' Donovan; A Thompson, F McNamara; K Griffin, S Cronin, C Costigan, P O'Brien, F Walsh, A Quinlan, C McMahon, D Quinlan.
Replacements used: D Ryan for O'Brien, G McNamara for Griffin, J Manuell for O'Donovan.
Referee: Mark Hermin (Ulster)