Peter Vincenti netted after three minutes after he prodded in from close range at the back stick, before Marc McNulty's free-kick from 22-yards on the stroke of half-time left Town with a mountain to climb.
The result sees the Town remain second, a point off Accrington Stanley at the top of Sky Bet League Two.
Jones said: "Yes it was [a game of two halves]. We were nowhere near in the first half. We didn't get to grips with it, we didn't pass the ball well enough, we didn't keep the ball well enough, we didn't defend well enough. We didn't do anything well.
"Then to concede after a minute from poor defensive play, so we were really disappointed. At half-time we didn't rant and rave, we knew we had to find a solution and not add to the problems and in the end we changed to a diamond and we were better in the second half.
"They could have nicked it, we could have nicked it. Jack Stacey had a great chance but we were much more like the threat and the team that we are. We played with energy. These have got the best defensive record in the league, but to score two goals and claw the game back was wonderful."
Jones celebrated with the supporters at the end of the game after his side battling performance. Asked what his message to supporters was for the final nine games of the season, he said: "Stick with us. There's going to be twist and turns. We have given them [the supporters] a hell of a season so far. We have given them enough football, enough goals, enough entertainment to earn a bad performance now and again.
"We gave them a half and they weren't happy about it, but they've got to stick with us.
"We work tirelessly every day. I am a passionate manager and I work tirelessly. But now we need them to get behind us, they might need to drag us through the odd game now and again because they're a good group and an honest group.
"We make mistakes, but that's the league, that's the level and that's what happens. If they want to get out of this level, then they have got to play their part and they have done tonight, second half they were magnificent tonight."