Moore rejoined Rovers in early March and led Rovers to a six-game unbeaten run and six wins in his first 10 games in charge, helping the club into mid-table in League One.
Moore said: "When I came back to Tranmere in March I said that I wanted to get the club to the 50-point mark before I discussed a contract.
"I'm delighted we have been able to do it with a few games to spare and even more delighted to have signed my contract. Now I want us to finish the season on a high and get as many points as possible in our final three matches.
"Everybody knows how big a part Tranmere Rovers has been in my life as a player, coach, caretaker manager, assistant manager and manager and I'm looking forward to the next 12 months.
"I want Tranmere to be a top-half team next season and I'll be looking to improve the squad over the summer. A big part of that comes down to how big our budget is and that comes down to season-ticket sales, so the more supporters we can get buying season tickets the better it should be for everyone."