Jones, who is former Wigan player and assistant manager, said: "I said pre-match, I didn't care who we were playing today.
"I've got a big affinity with Wigan Athletic, but you've got your own professional pride to fight for and whoever was in the way, we needed to find a way. It came late and it came from two subs, but we found a way.
"The mentality has never been in question, I just think we got caught with our pants down last week, arousal levels were maybe low coming to Brentford, especially having to push so hard and concentrate so much against Leeds and Charlton.
"I feel like we fell of a cliff mentally after the game but you can't afford to as this league is punishing and that was the definition of it.
"I don't ever want to go back to that situation but what mattered today was the result and I think we got a performance with that, not just the result.
"I had 10 players out of the 11 who started last week, Izzy Brown had a genuine injury, who presented themselves ready to play, no excuses.
"Now when you do that and it's tough and you have to dig in and you have to learn and you get better, so there's been a lot of satisfying aspects."
It had looked like Wigan would pick up a first away victory in the Championship this term after leading through Kieffer Moore's 35th-minute strike, finding the net from Dujon Sterling's cross with a bullet header.
Town, who had missed a hatful of chances in the first period, then hit back with three minutes left, McManaman netting from close range.
Wigan boss Paul Cook, who saw his side slump to an eighth successive game without a victory, said: "It's like watching the same film over and over again when you already know the ending.
"I've never criticised the players, ever, and I'll stand by that.
"The reality is that managers carry the can for players.
"I'll carry on doing that while I manage the club because I think that's the correct and proper thing to do.
"We do the same things. It's like playing pass the parcel – you've got the prize in your hand and you let it go.
"I'll take the blame for everything, it's repetitive and boring. If you don't retain possession in the opposition's half the reality is they will get on top and hurt you. And we continually gave the ball away.
"People say it can't rain forever but it's not doing a bad job at the minute.
"We have a habit of games not going our way at that most crucial point, and that's heartbreaking, as we're not learning."