After losing their last three matches in their worst ever start to the season, Gibson revved up his troops, who were trailing 25-6 at AAMI Park, and they responded with four second-half tries to snatch the victory.
It was sealed in the 80th minute when the Waratahs took advantage of the Rebels losing Colby Fainga'a to a yellow card and Sefa Naivalu down with a dislocated shoulder.
Centre David Horwitz ran on to a Nick Phipps pass and threw a dummy before scooting through some skinny defence for the match-winner.
A 77th minute try by Michael Wells, converted by Bernard Foley, had locked up the match at 25-25.
Waratahs skipper Michael Hooper said Gibson was clear with his halftime message.
"He said our season was on the line and we were up against it and we came out and threw some punches," Hooper said.
"We were shooting ourselves in the foot, making mistakes, letting them get on to the ball.
"We were seeing the penalties mount up and Reece Hodge knocking them from everywhere and it was not a good position to be in."
Despite the large half-time deficit Hooper said there was still plenty of belief in the change room they could take the result.
"I felt really confident that we could manage to get back to back points in the second half.
"I also felt we played some really good footy in the first 10 minutes and were one pass away from walking over the tryline in the first half a couple of times so it wasn't like it was solely a second half effort."
The Waratahs host the unbeaten Crusaders next Sunday and Hooper felt they would take confidence into the match.
"It's pretty rewarding; we spoke about the position we were in at halftime and then to come out and break out of the shackles and do what I've been speaking about at training... it was a good grinding win."