Latics qualified for the last 32 of the Papa John’s Trophy despite defeat in their final Northern Group B fixture at Prenton Park.
Zak Dearnley struck twice to give Latics a two-goal lead at the end of the first half, but having conceded in added time, Kieth Curle’s side saw Tranmere complete a turnaround after the break.
The home side topped the group ahead of the game and victory for the hosts means they progress as group winners. Having finished with an identical record to Salford, Latics progress by virtue of their head-to-head result, meaning they will feature in the draw for the next round on Saturday afternoon.
Victory against Salford in the opening group game meant Curle’s side occupied second place going into the closing game of the opening stage. The Head Coach made four changes from the Emirates FA Cup draw at Ipswich, including a first start since August for Nicky Adams following his recovery from a hamstring injury.
It looked good for Latics when Dearnley opened his account after 15 minutes, showing great composure to apply a measured finish as he stroked the ball past Joe Murphy having been played clear by a measured pass from Davis Keillor-Dunn.
It was Tranmere who started the sharper but once ahead the visitors proceeded to take control, Keillor-Dunn’s 20-yard effort taking a deflection wide, while Faysal Bettache found Carl Piergianni inside the area but he was unable to keep his effort down.
Nicky Maynard had two early chances for the home side, who then saw Kieron Morris clear the crossbar with a free-kick.
But it was Latics who continued to force the issue, Benny Couto lining up a fine first-time strike after a sweeping cross-field pass from Adams, only for the shot to be diverted wide.
Dearnley added his second late in the first half to finish a sweeping Latics move, Keillor-Dunn releasing Adams, whose brilliant cross from the right was converted by the forward’s bullet header.
Glaztel nodded in cross from Ryan Stratulis to halve the lead in first-half stoppage time, and although Dearnley and Piergianni had chances at the start of the second period, the home side drew level.
Maynard restored parity with an angled finish after receiving a pass from Glatzel, as the momentum turned in favour of the home side.
There were still chances for Bahamboula and Adams, both of whom were denied by goalkeeper Joe Murphy, but with Tranmere in the ascendancy they secured the win on 75 minutes, Glatzel adding his second from inside the area.
Oldham Athletic: Leutwiler, Clarke (Whelan46), McGahey, Piergianni, Adams (Fage 63), Keillor-Dunn (Hope 63), Couto, Bahamboula, Dearnley, Bettache, Diarra.
Subs not used: Southerington, Bowden, Da Silva, Modi.
Tranmere Rovers: Murphy, Knight-Percival, Davies, Morris (MacDonald 89), Glatzel, Maynard (Dieseruvwe 89), Walker, Duffy, Maguire, Stratulis.
Subs not used: Doohan, Watson, Nevitt, Jones, Dwyer.
Referee: Marc Edwards
Attendance: 1,405 (125 away)