Kurtis Guthrie gave Colchester the lead against the run of play just after half-time, but two late goals from Francois Zoko and Tahvon Campbell turned the match on its head.
The win extended the Glovers’ unbeaten league run to six matches and Way feels his side were deserving of their victory.
“We were very dominant,” he told YTFC’s official YouTube channel.
“It was a really pleasing performance from start to finish.
“We got into the final third about 28 times and had 12 or 13 crosses go into the box, four of which flashed across the six-yard box.
“You start thinking ‘is the ball really going to go in?’.
“They’re a special group. They kept going, never gave up and kept fighting.
“We kept going and remained positive. I enjoy seeing the supporters go home happy because it makes me happy and you never know where we can keep climbing.”
He added: “It’s been quite an emotional week for me as a manager.
“In my ten months in charge, the defeat to Solihull was probably my lowest and probably the group’s too.
“The conversation we had before we left the dressing room to get on the bus was can you show character and personality this week and what I’ve seen is unbelievable character, personality, fight and spirit to win the game.”
At this stage of last year’s League Two campaign, Yeovil were in the relegation zone with just 10 points.
A year on and Way’s side are on more than double that total and continue to strive towards a play-off place.
“We’ve made massive progression since i took over,” he said.
“This time last year we were on ten points so that’s a big difference and transition.
“We’re doing things right at the football club.
“The staff have been very loyal to me and have worked their socks off so I’m pleased in every department. We’ve just got to keep driving.”
Town’s next match sees Crawley Town visit Huish Park on Tuesday, November 22nd (7.45pm).
Fans can purchase tickets for the match online or by phone on 01935 847888.