Waterford made heavy weather of booking their berth in the third round as they almost blew a 2-0 first half lead.
Skipper Daryl Murphy headed Blues in front after just two minutes to punish some dreadful defending.
Murphy was there again to add a second goal on 35 minutes from Dave Mulcahy’s assist but Stephen O’Donnell gave Rovers hope with a penalty on 52 minutes.
Blues were hanging on at the death after Mark Clifford was sent off for a second booking 12 minutes from time.
Filed by Barry McEneaney
