Bowery struck in the 76th minute to leave Tranmere without a victory in 2012 and anxiously looking over their shoulders.
Chesterfield had not scored in their previous two games, but looked certain to take the lead in the 38th minute when a short back pass let Jack Lester in only for Rovers defender Ian Goodison to make a sliding goalline clearance.
Tranmere were rescued again in the 51st minute by a plunging save from goalkeeper Owain Fon-Williams to keep out a 25 yard drive from Nicky Ajose.
But the visitors forced Tommy Lee into his first serious save via Andy Robinson's near post shot in the 71st minute.
But the home side finally made the breakthrough five minutes later when Lester's precise pass set up Bowery to drive a low shot from 12 yards past the right hand of Fon-Williams.
Any reproduction, publication or redistribution of this material without the written agreement of 365 Media Group is strictly forbidden.