Rovers were second-best throughout, but referee Eddie Ilderton gave a spot-kick in the 94th minute when he deemed Oldham keeper Mark Oxley to have fouled Lowe.
The striker stepped up to send Oxley the wrong way and Oldham boss Lee Johnson was sent to the stands for his protests.
Tranmere’s only previous chance had come in the 82nd minute when Ash Taylor’s header drifted wide.
Oldham created several openings and could have led inside two minutes when Jonson Clarke-Harris sent a free header off target from James Dayton’s cross.
Adam Rooney and James Tarkowski also went close and Oldham had penalty appeals waved away when Tarkowski seemed to be dragged down by Ian Goodison.
Oldham missed another good chance through Albert Rusnak, but Tranmere had the final say to earn their first league win since March.