Steven Naismith gave the Premier League outfit a half-time lead when he got on the end of Luke Garbutt's cross to finish from close range 26 minutes in at Prenton Park, before Roberto Martinez made 10 changes at half time, with the likes of Darron Gibson and Seamus Coleman introduced.
Gibson had been sidelined since October after suffering cruciate knee ligament damage playing for his country, but he came through 45 minutes of the Toffees' first pre-season friendly against the League Two side.
Tranmere were not overawed by their more illustrious opponents in the fixture and levelled when Cole Stockton sent a fine chip over goalkeeper Joel Robles.
Leon Osman looked to have won it for Everton 18 minutes from time when he was on hand to turn home following a corner, but James Rowe struck with only three minutes remaining after his initial effort had hit the post.
Coleman was withdrawn in the second half as a precaution, but Gibson's return is a major tonic for Everton ahead of the new season.