The Republic of Ireland midfielder had been sidelined since October after suffering cruciate knee ligament damage playing for his country, but he came through 45 minutes of Everton's first pre-season friendly against the League Two side.
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.
Everton boss Roberto Martinez fielded 10 different outfield players in the second half, with the likes of Gibson, Seamus Coleman, James McCarthy and John Stones introduced.
Tranmere were not overawed, though, and they levelled when Cole Stockton sent a fine chip over 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Coleman was withdrawn in the second half as a precaution, but Gibson's return is a major tonic for Everton ahead of the new season.
After the match, Martinez confirmed that he was considering a move for 18-year-old Anderlecht forward David Henen.