An injury time strike from Alex Cooper saw Rovers over the line at home in the Showgrounds.
The win moves Liam Buckley’s side two-points clear of the bottom two.
Waterford got the better start, with Michael O'Connor netting in the 16th minute.
The Rovers revival didn't come until the second half, with Ronan Coughlan allowing the home side to pull even after 77 minutes.
Coopers last gasp goal three minutes into injury time sent the socially distanced crowd singing, giving them the favourable outcome with maximum drama.
The crowd in the Showgrounds will be one of the last groups of sports fans cheering on their team on person as new Government guidelines will see all sporting events being held behind closed doors until September 13th.
Taoiseach Micheál Martin announced the new measures in an attempt to combat the spread of Covid-19 here.
While training and matches can continue to go ahead, the number of spectators permitted to attend will drop from 200 to zero effective immediatly.
