Just two minutes in Berry went down with what we have been informed is a dislocated ankle, with a suspected fracture and possible ankle ligament damage.
There was a long hold up in play before Tom Eastman headed in shortly after play resumed, before Luke Prosser scored in similar circumstances to double the hosts' lead just before the half hour mark.
Luke Gambin was brought down by Ryan Jackson in the penalty area which Danny Hylton converted from with two minutes of normal time to play, but the U's held out for the three points.
Jones said: "It's sad. He's gone over on it, we don't know how he's done it. There's a few little things I don't want to say because there were a few things we weren't happy with before the game. I don't know if that was contributing factor but we will see.
"It's a bad injury and one that will keep him out for a while, we don't know the full extent but it's a sad day really because he's been in great form, he's a great kid and he's a wonderful player for us and our best wishes go out to him, but we will make sure we will look after him and get him back as quick and as safe as we can.
"They [the players] came in and they were shocked and I had to try and lift them. They were down and they were shocked and one of our players were sick. It doesn't bode well.
"Best thing we could have done for him was to win the game and that's what we didn't do, we didn't recover from that and uncharacteristically we conceded two from set-plays. They were basic, it wasn't exactly a greatly worked thing, it's a lofted ball. It was just lazy defending and that's what cost us.
"I cant remember them having a lot of chances. We weren't at it first half, we changed shape which we don't like doing, but we felt we had to do it and those two goals, the lapses of concentration is what cost us in the end."