Brian Murphy produced a brilliant save from Michael Duffy after 14 minutes.
Man of the match Jake Davidson came to Waterford’s rescue with a fine clearance when Michael Duffy was about to shoot inside the penalty area.
Daryl Murphy almost put Waterford in front five minutes before half time, but his low shot from 16 yards went inches wide.
John Martin put Waterford in front on 57 minutes, when he headed home a left wing cross from Will Fitzgerald.
Ali Coote was the player who had picked out Fitzgerald with a superb free kick from the right.
Daryl Murphy ran on to a long ball from his namesake Brian Murphy on 78 minutes but his shot on the run was saved by the Dundalk goalkeeper Aaron McCarey.
Dundalk huffed and puffed for the remainder for the game, but the closest they came was five minutes from full time when Patrick Hoban crashed in a low shot from the left, but the ball whistled wide off the far upright.