Lowe fired Tranmere in front after just seven minutes and then pulled them level just after the hour from the penalty spot after Daniel Powell and Jason Banton had put the Dons 2-1 ahead.
And with six minutes remaining, Rowe, on as a substitute, met Jake Kirby's lay-off to give Rovers a first home league win and just their second victory in their last 11 fixtures in all competitions.
Lowe capitalised on a poor Shaun Williams back header to fire Tranmere in front, racing on to the loose ball before lobbing it over a stranded Ian McLoughlin.
However MK Dons were level in the 39th minute as Powell went on a surging run from midfield and lashed home, while Banton unleashed a dazzling strike to give them the lead shortly after half-time.
James McNulty should have drawn Tranmere level but Lowe did not make any mistake from the spot after the former had been pushed to the ground by Jordan Spence.
Patrick Bamford missed a glorious chance to restore the visitors' advantage moments later and Rowe took full advantage with the winner.