Otis Khan's goal ensured Tranmere clinched their first away win of the season during their seventh road trip of 2020-21.
Substitute Khan struck in the 79th minute as Rovers, with coaches Ian Dawes and Andy Parkinson in caretaker charge following Michael Jackson's sacking, took the Sky Bet League Two spoils at Harrogate following a 1-0 triumph.
Six-goal Rovers top scorer James Vaughan was a hero and villain for the visitors in the first half.
The former Everton striker prevented his team from falling behind as he headed George Thomson's inswinging corner - one of nine won by the home side in the opening 45 minutes - off the line.
But, in stoppage time before the break, Vaughan should have opened the scoring at the other end when he raced clear on the home goal - only to strike an upright.
After the break, home keeper James Belshaw reacted smartly to stick out a leg and keep out a near-post Paul Lewis effort.
Vaughan and fellow veteran Jay Spearing also went close from distance, before Khan made the breakthrough.
The former Sheffield United and Yeovil winger calmly sidefooted inside Belshaw's left-hand post from 10 yards after Liam Feeney's low left-wing cross struck team-mate Lewis and fell fortuitously to him.
In the 11th of 14 minutes of added time, chiefly caused by lengthy treatment for a concerning injury to home defender Will Smith - who was carried off - Tom Walker should have levelled but scuffed an easy chance with the goal at his mercy.