The 23-year-old was originally named in the team at Craven Cottage, but withdrew moments before kick-off after complaining of a tight hamstring, Dan Potts taking his place in the starting XI, with Kal Naismith moving back to midfield again.
The summer signing from Motherwell hadn’t wanted to miss out, but Jones conceded it was for the best with one eye on this weekend’s play-off decider against Reading coming up.
He said: “It was more precaution than serious.
"If I let him he would have played and I made the call and it was the right call, because if he had played and broke down, we didn’t want to gamble.
“We can’t gamble in midfield because we haven’t got many to replace them and that’s the issue we’ve had
“Hopefully we will be as strong as we possibly can, but whenever this group have to perform they do.”
The Scot has been one of the top performers for the Hatters this term, winning a number of plaudits for his displays in the midfield, also voted the Luton News Player of the Season by supporters this week.
On just how much Town missed him at Craven Cottage, Jones added: “I think a number of players have done so well this year that we miss them.
“We’ve been without a lot of big players. For Fulham the other day, we said had arguably six or seven starters missing and no side can maintain that.
“It is going to be important we try to get some back because we need that.
“If we weren’t hindered enough in terms of budgets compared with someone like a Fulham then to have six, seven players out is tough.
“A lot of things went against us in terms but we have to make sure we are just focused on one game now.”