Vinny Sullivan missed a glorious late chance as Waterford had to settle for battling it out in the play-off to stay in the Premier Division.
Blues got the point they needed to avoid automatic relegation, but as UCD lost in Galway, victory would have seen them completely safe.
And they left Tolka Park ruing Sullivan's 87th minute missed opportunity.
It stemmed from a break down the right by Willy John Kiely whose low cross appeared set for a simple tap in from the in-rushing Sullivan.
But the striker took his eye off the ball and had a 'fresh air' dead in front of goal - a miss that can only haunt him all week.
It means that Gareth Cronin's side must run the gauntlet of a two-legged play-off with the winners of the second versus third play-off in the First Division to secure their place in next year's Premier Division.
Waterford fielded the same side as earned a draw with Galway United at the RSC last week.
But unlike in that game, when they didn't really perform, Blues were focused from the start and produced the first real chance of the night on nine minutes.
Dave Warren's deep diagonal ball from the right bounced through to David Breen at the back post, but his looping header was over the top.
Another Warren delivery, but from much closer in, six minutes later asked further questions of the Rovers defence.
This time skipper John Hayes was left unmarked, but, perhaps not realising the time he had, placed his glancing header wide of Barry Murphy's right-hand post.
Murphy had to show why he one of the best young keepers in the Premier Division from another Blues assault ten minutes before the break.
It was all his own work, as Willy John Kiely burst forward down the left flank to cut inside a defender and unleash a powerful drive that Murphy had top push away two-hand and at full stretch.
Rovers hit back on the counterattack within seconds.
Owen Doyle was played in down the inside right channel but his finish was poor and his weak shot was comfortable for Dean Delaney.
It was set-pieces that were bringing the bulk of the chances in a desperately dour game.
Warren again was instrumental for Blues nine minutes into the second half when picking out Breen from a corner. But the big defenders header was hacked away for another corner by Barry Ferguson.
Ger Rowe replaced Andy Myler for Rovers on the hour mark and added some urgency to their attack, almost breaking the tedium with three minutes.
Collecting a cross field ball, Rowe skipped inside and brought a diving save from Delaney from 25 yards.
That livened up Rovers and one of the few decent passages of football almost brought them the lead on 70 minutes.
Chris Mulhall was put away down the right and put over a good cross. Rowe met it and his spectacular overhead kick was inches over Delaney's bar.
Rowe was there again four minutes later. This time the striker got on the end of David Cassidy's free-kick in from the right, but just could get any significant purchase on it and it glanced well wide.
Shamrock Rovers: Murphy; G. O'Brien, Danny O'Connor, Ferguson, Clarke; Creevy, Cassidy, Shiels, Tyrrell (Mulhall, 53); Doyle (Kilduff, 65), Myler (Rowe, 61).
Waterford United: Delaney; Flynn, Hayes (Browne, 89), Breen, Hedderman; Scully, Warren, D. Mulcahy, McCarthy; Kiely, Sullivan.
Referee: Pat Whelan (Dublin).
