The former Brentford holding midfielder was substituted just before the half-hour mark at the ABAX Stadium, with Glen Rea coming onto replace him.
McCormack missed a majority of last season after suffering from groin and calf problems, playing 16 times in his debut campaign at Kenilworth Road.
Jones said: "We will pick a side tomorrow that we feel can win the game. Some will be enforced changes – we have one enforced change. So whether we make changes or not, it will be for the good of Luton Town and that's what we're looking to do.
"Anytime Macca feels that, it's a precaution because we know he is susceptible to picking up a serious injury. We had to make the change at the right time and fortunately we had Glen Rea to have brought in there.
"It's not a serious calf injury or anything, we've dusted them down today and then we go again tomorrow. We're in decent shape, obviously we will have bumps and bruises from the encounter with Peterborough, but they will be ready."
Luke Berry is edging closer to a return to regular action having made his first appearance of the campaign in the 1-0 loss at West Brom last Tuesday. Jones isn't expecting the 26-year-old to fully feature just yet, but hopes to see him get more time in the foreseeable future.
"He needs minutes, he needs games. It was good to give him minutes against West Brom, but to put him into a league game where we're expecting to get big minutes out of him, then he needs just a little bit more time. That's what we will give him now this month."
Tomorrow, the Hatters host Southend United, who are managed by former Charlton boss Chris Powell – with the Hatters first team staff having strong links with the Addicks, as Jones, as well as assistant manager Paul Hart and head of sports science Jared Roberts-Smith all worked under the former England full-back.The gaffer was Under-21 boss for a season at The Valley, before becoming assistant head coach at Brighton & Hove Albion in 2013.
"I owe Chris quite a lot to be honest, one of the nicest guys you'll ever meet," Jones continued.
"Obviously he's doing a real good job there, he did a good job when he was at Charlton, I loved working for him.
"He gave me a real opportunity there, I worked with Harty as well there, but Chris was a big influence on me. He gave me the autonomy and the decision-making mobility that I could control that group and I think I repaid him by producing players for his first team.
"I loved working for Chris and I am looking forward to seeing him."
Watch the gaffer's full pre-Southend United press conference now by clicking play on the video above.
