Moore replaced outgoing boss Les Parry in March to take the reins for a third time at Prenton Park with Rovers in danger of relegation from League One.
However, a run of six wins and three draws in 11 games under Moore shepherded the Merseyside outfit to safety and the 59-year-old has agreed to remain in charge next season.
Johnson said: "I'm delighted Ronnie will be staying as our manager.
"He has done a wonderful job in securing the club's League One status for next season and has led us to one of the best records in the division over the last couple of months.
"I'm sure he will help the club progress further in 2012/13. He has a great rapport with our fans and I'd like to thank them for their fantastic support since his return."