Dean Walsh's struck a spectacular volley four minutes from time to consign UCD to further relegation woe and all but guarantee the Blues’ Premier Division survival for another year.
The substitute had only been on the pitch for 12 minutes, having replaced the ineffective Michael O’Connor, when he sent John Kavanagh’s crossfield ball arrowing back into the far corner.
It was rough justice on UCD and 18-year-old goalkeeper Tom Murphy, making his first-ever senior appearance, but they paid the price for a sluggish start that saw them trail inside seven minutes.
Ireland under-21 international Zack Elbouzedi put the Blues in front early on, before Liam Kerrigan equalised on his debut, but Walsh struck late to earn Alan Reynolds’ side their first win in six.
Winger Elbouzedi had been laid low since injuring his shoulder playing for Ireland under-21s at the Toulon Tournament in June, but showed few ill-effects as he immediately found his scoring touch.
He took the ball out wide and danced inside the tackles of two UCD defenders before opening his body and bending a shot into the corner past the helpless Murphy.
The Blues had survived a big scare just 30 seconds earlier as Liam Kerrigan, one of three UCD debutants following his move from Sligo Rovers, forced Matthew Connor into a smart save.
The midfielder showed good strength to wrestle former Student Maxi Kougun off the ball in the box and found room for a shot, but Connor was out of his goal quickly to cut off the angle.
UCD had paid the price for their slow start but they went on to dominate the rest of the half, with the former Sligo pair Kerrigan and Jack Keaney particularly prominent.
Kerrigan had a trio of chances during the first period, the best a fine curling effort that had Connor at full stretch to claw it out of the corner.
Waterford might have doubled their lead just before the break as Rory Feely’s deep cross needed to be dealt with by Evan Farrell, whose attempted clearance clipped the top of his own bar.
From the resulting corner, Kouogun dug the ball out of his feet to tee up JJ Lunney, but the former St Patrick’s Athletic man could only shoot straight at Murphy.
Connor was in fine form in goal for the visitors and he showed incredible reflexes to get low to save a Paul Doyle shot that looked destined to burst the net.
He might have done better to deny Kerrigan when the debutant took Paul Doyle’s pinpoint pass on the left, cut inside and drove a firm shot past Connor at his near post.
All the momentum was with UCD at that point and they looked the more likely to take the three points, but Walsh had other ideas and he sent the large travelling support wild with a late volley.
UCD: Murphy; Farrell, Scales, Dignam; O’Farrell, Keaney, Doyle (Kinsella Bishop 90+1), McClelland, Dignam; Kerrigan (Ryan 83), Byrne (Mahdy 80).
Waterford: Connor; Feely, Kouogun, Slevin, Kavanagh; Duggan (Poynton 83), Lunney, Holland; Galvin (Chvedukas 61), Elbouzedi, O’Connor (Walsh 74).
Referee: Paul Tuite.