Johnson still has an interest in Rovers, whom he left to take charge of the Goodison club in 1994. League rules bar an individual from having control of different clubs and a League spokesman said: "The Football League has confirmed that it has given a company owned by Peter Johnson, chairman of Everton, limited consent to hold a major interest in Tranmere Rovers.
"Mr Johnson acted correctly in seeking the prior consent of the Football League board. This was granted conditionally on him disposing of one of his clubs by January 1, 1999 and seeking prior consent for any player transfers or loan dealings between the two clubs.
"This action was taken to protect Tranmere and to establish immediate financial stability whilst an orderly sale was arranged. The League is sure that supporters of Tranmere will be grateful for this intervention."
A Premier/Football League Commission will be set up if Johnson does not sever his ties with either club by the end of this year - it can do anything from impose fines to relegating both clubs.
The Northampton Town manager, Ian Atkins, is facing a Football Association enquiry into an altercation with a rival manager, David Moyes, at the end of a stormy match.
Atkins allegedly grabbed Moyes, the Preston North End manager, by the throat in the middle of a melee at the final whistle of Saturday's Second Division fixture at Sixfields - and he could be banned from the touchline for the rest of this season.
Both sets of players were involved in scenes of mayhem after Northampton's injury time equaliser in a 1-1 draw.