The 20-year-old centre-back impressed in 25 appearances for Rovers earlier this season, winning 13 and drawing seven games before injury curtailed his first spell at Prenton Park.
In a club statement, manager Ronnie Moore said: "I'm really pleased that we've been able to bring Ben back to the club.
"We had hoped to have him all season but unfortunately he has missed three months with injury.
"But we've got him back now and he will strengthen our squad. He was fantastic for us in the first half of the season and hopefully he will pick up where he left off.
"He gives us leadership and calmness on the pitch and I'd like to thank (Middlesbrough manager) Tony Mowbray for allowing Ben to rejoin us."
Gibson added: "I've been looking forward to coming back to Tranmere since December. I loved my time at the club.
"I want to finish what I started. The lads have done so well to stay in the top six all season and I believe we can finish in at least a play-off place.
"I can't wait to get playing again and hopefully that can start with three points at MK Dons on Saturday."
Tranmere lie fifth in League Two, two points behind second-placed Sheffield United having played two games more, but have won two and lost six of their past nine matches.