The first half was a cagey affair, with top spot on the line for both sides after Forest Green's earlier defeat at Dover.
Tranmere goalkeeper Scott Davies had to be alert to keep Macauley Bonne's header out early on, while Luke Waterfall went close with a free-kick in the 25th minute, but the hosts also threatened through James Norwood.
Bonne, on loan at Lincoln from Colchester, got the crucial breakthrough in the 67th minute when he smashed into the roof of the net from Terry Hawkridge's cross.
Tranmere have now lost back-to-back games after starting the season with a seven-match unbeaten run.
Report supplied by the Press Association.
Match ends, Tranmere Rovers 0, Lincoln City 1.
Second Half ends, Tranmere Rovers 0, Lincoln City 1.
Terry Hawkridge (Lincoln City) is shown the yellow card.
Paul Farman (Lincoln City) is shown the yellow card.
Substitution, Lincoln City. Alan Power replaces Bradley Wood.
Substitution, Tranmere Rovers. Adam Mekki replaces Jay Harris.
Substitution, Lincoln City. Adam Marriott replaces Macauley Bonne.
Substitution, Tranmere Rovers. Darren Stephenson replaces Andy Cook.
Goal!  Tranmere Rovers 0, Lincoln City 1. Macauley Bonne (Lincoln City).
Substitution, Lincoln City. Harry Anderson replaces Nathan Arnold.
Steve McNulty (Tranmere Rovers) is shown the yellow card.
Substitution, Tranmere Rovers. Jake Kirby replaces Connor Jennings.
Bradley Wood (Lincoln City) is shown the yellow card.
Second Half begins Tranmere Rovers 0, Lincoln City 0.
First Half ends, Tranmere Rovers 0, Lincoln City 0.
Jay Harris (Tranmere Rovers) is shown the yellow card.
First Half begins.
Lineups are announced and players are warming up.
Lincoln are top of the National League after a win ended Tranmere's 100% record at Prenton Park this season.