Bowery, who had only been on the field for eight minutes, slid home a precise effort as he darted in to meet Rhys Oates’ cross.
Nigel Clough’s Stags deservedly triumphed as they ended their mini-blip of rare back-to-back defeats.
It was a first win at Rochdale since April 1997 – 12 visits ago – Stags having lost 10 and drawn one of their last 11 games there – hardly a happy hunting ground.
Mansfield were given a huge boost with the return from injury of key midfielders Stephen Quinn and Matty Longstaff.
There were also returns to the starting line-up for defenders Elliott Hewitt and John-Joe O'Toole as boss Nigel Clough made four changes.
Farrend Rawson, Keiran Wallace, George Lapslie all dropped down to the bench and Ollie Clarke missed out with injury.
The Dale side included ex-Stag Corey O'Keeffe.
The third of five consecutive away fixtures for the Stags saw an enterprising start at a misty Crown Oil Arena.
Stephen Quinn found space just outside the box, only to see his shot deflected off target.
The hosts replied with target man Tahvon Campbell charging through the middle before driving a disappointing effort high over the top.
Stags keeper Nathan Bishop was then alert as he kept out a powerful strike from Jimmy Ball.
The visitors kept plugging away and came close to an opener in the 24th minute when Jamie Murphy fizzed in a shot which only just cleared the crossbar.
Oates then ought to have done better when he made a super break into the box before firing frustratingly straight at ‘keeper Jay Lynch.
The Stags were getting on top as half-time approached, but an end product was missing.
Oates almost found it in the 40th minute, but again Lynch was equal to the task with a smart stop.
Continuing the theme into the second period, Oates tested Lynch yet again with a crisp effort soon after the restart.
Rochdale had been second best, but they almost made the breakthrough when Matt Done forced Bishop into a decent save.
Paul Downing also went close as the hosts were looking to build some momentum, but back came the Stags with Murphy firing inches wide of the far post following Elliott Hewitt’s measured through-ball.
It was left to Bowery to seal the points for the Stags with his cool finish finally breaking Rochdale’s resistance.
O'Toole began the move with a fine pass to Oates wide on the right. And he sent in the perfect low cross for Bowery to net Stags' first goal in five trips to Rochdale from close range, firing high into the net, and set Mansfield up for a return trip to the North-West on Saturday with a game at struggling Oldham, who lost 3-1 at home to Sutton United.
Stags remain in 10th place in League Two but are only two points off the top seven and four points off the top three with three games in hand on most of their rivals and their fate in their own hands.
ROCHDALE: Lynch, Downing, O’Connell, Dorsett, O’Keeffe, Broadbent, Dooley, Clark, Ball (Grant, 41), Campbell (Newby, 63), Done (Charman, 85). SUBS NOT USED: Coleman, McNulty, Keohane, Kelly.
STAGS: Bishop, Hewitt, O’Toole, Perch, McLaughlin, Stirk (Lapslie, 82), Longstaff, Quinn (Wallace, 73), Murphy (Bowery, 78), Hawkins, Oates. SUBS NOT USED: Stech, Rawson, Maris, Johnson.
REFEREE: Seb Stockbridge.