The England international, out since the beginning of February, was unable to make any real telling difference on his return to action as the Red Devils dragged their way to victory.
Paddy McNair hit the winner 67 minutes in to earn United three valuable points, taking them within two of leaders Sunderland with three games in hand to play over their opponents.
The first half was largely bereft of any real entertainment, with the big talking point arriving 35 minutes in when Boro skipper Jonny Burn - sent off in the reverse fixture - lunged in on Joe Rothwell with a horror challenge.
Burn caught his opponent high on the shin with his lunging tackle, forcing the United midfielder to limp off soon after, but the incident incredibly went unpunished by the referee.
While the Red Devils were largely in control of the opening 45 minutes, the best chance arguably fell the way of Arnel Jakupovic early on, yet Sam Johnstone's outstretched leg denied the striker a breakthrough goal when played through.
The 7,000 or so United fans inside the Theatre of Dreams had to wait until the final act of the half for their only other shot of the opening 45 minutes, with Devonte Redmond's curled effort easily kept out in the end.
With the onus on title-chasing United to find a way through in the second half, the message from boss Warren Joyce was clearly to get more shots on target.
Andreas Pereira, on for the injured Rothwell in the first half, blasted in a strike from all of 35 yards out which was simple enough for Fryer to get behind between the sticks.
The scene appeared to be set just short of the hour mark when Rooney stepped up to take a free kick in perfect shooting range, which he subsequently fired a good few metres wide of the target.
Rooney's comeback came to an end just over 60 minutes in, following a performance that showed the odd glimmer of his attacking qualities but not enough to make any real impact on the game in the final third.
United continued to push for a winner in the remaining half-hour of the match, coming close to doing so through Donald Love's well-hit strike which Fryer again did well to get fully behind.
The breakthrough finally arrived 23 minutes from time when McNair controlled a cross from the right with his first touch and blasted home with his second for his fourth goal in 14 outings at this level.
Pereira almost added a second late on when cutting onto his right and sending a swerving shot back off the upright, leaving Fryer beaten but denied only by the frame of the goal.
That ultimately proved to be it in terms of chances for either side, meaning an opportunity missed for the visitors to pick up a much-needed point in their battle to beat the drop.
Meanwhile, defeat for leaders Sunderland against Tottenham Hotspur elsewhere in their final match of the season ensures that the Red Devils are now within one win of back-to-back titles.