Gary Mills netted his first goal for Rushden & Diamonds to give them victory at Nene Park.
Onandi Lowe fired Rushden in front with a brilliant 49th-minute effort that flew in off the post.
Tranmere levelled when Danny Harrison headed in Ryan Taylor's cross and almost went ahead when top scorer Eugene Dadi struck the upright.
Mills exchanged passes with Lowe and fired in the winner before Tranmere's Iain Hume hit the post late on.
Rushden & D'monds: Ashdown, Bignot, Edwards, Hunter, Underwood,
Hall, Bell, Mills, Gray, Jack, Lowe. Subs: Hanlon, Dempster,
Sambrook, Duffy, Talbot.
Tranmere: Achterberg, Goodison, Allen, Linwood, Taylor,
Harrison, Beresford, Roberts, Mellon, Hume, Dadi. Subs: Jones,
Nicholson, Howarth, Navarro, Hay.
Referee: T Kettle (Maidenhead)