The skipper slipped awkwardly in the victory over the U's and had to be stretchered off, with the Scotsman expected to be on the sidelines until January.
Jones said: "Scott's going to be out for a little bit of time because he's had a slight tear in his adductor on the right side, and then on the other side – which we more fearful about – there isn't a problem. So there's going to be a few little things going on in there, but all those will heal by the time his adductor heals.
"Basically we are going to miss him throughout the Christmas period and we will get him back for January in God's will."
Jones spoke of his frustration after his side's 0-0 draw at Crawley Town back in October, as he felt his team could have done with a couple of changes having beaten Stevenage and Exeter City prior to the stalemate at the Checkatrade Stadium.
He explained he will use that experience to ensure his team will be at their best as he plans to use the depth of his squad when they play at Gresty Road on Saturday.
He said: "We have talked about that, about eradicating it and using the squad – and that's a real possibility. We have had big efforts this week, the one thing that's different is we had the big journey on the Tuesday [back from Exeter] and got back on the Wednesday, so that kind of added to everything.
"We will see how they are. We have dusted them down today, most of them have had a session, the others have a second day of recovery, so we get them in to good energy for tomorrow for a training session and then the journey there.
"It's going to be a tough game, we know that. But we couldn't go into the game in any better form."
Tuesday evening's victory over Carlisle United saw the Hatters keep their ninth clean sheet of the season, with Jones happy with the foundations his team now have in place.
"I am most pleased with a win" he continued. "I think the way we are going about our work, our work rate at the moment, the discipline we are showing in terms of our defensive discipline is excellent.
"Obviously the goals we are scoring are going to get the highlights and the accolades, but our foundation is built on hard work and hard graft, and a lot of our goals have come from that – of us pressing it high and winning it.
"So that's what we work hard at. That's our foundation."
Town once again scored from a set piece in the 3-0 victory over the Cumbrians, something Jones admitted he hasn't been directly involved in on the training ground, but praised a couple of his first team staff for adding another dimension the Hatters' forward line.
Jones said: "It's a credit to Paul Hart and to Joaquin Gomez. I have an eye on those, but they really work hard on them and they take them aside and take control of that element. The players themselves asked for an extra session for us to put in place, but I don't think anything is a fluke.
"I don't care what people say about us, we work hard on every aspect of our play. It's a good group and the reason we are reaping benefits from many aspects of our play is because we work hard at it."
