Allen was forced to miss the defeat against Norwich as he struggled with a hamstring strain and Rodgers felt his influence in midfield was badly missed.
The midfielder had an outside chance of playing but Rodgers was unwilling to take a gamble in case he made the problem worse, but he should be fit for the clash against the Potters on February 26th.
Allen is now set to return to training and Rodgers says he will be delighted to have him back in the side.
“There’s no doubt that we missed Joe last weekend ? and that’s the reason why I rested him,” Rodgers told walesonline. “He is very important for us. He is such a catalyst for our team, both with the ball and with our pressure off the ball.
“We could not afford to lose him for six or seven weeks, and that’s why we didn’t play him against Norwich. He maybe could have played, but I felt it would have been too big a risk.
“Joe will be training by the end of this week.”
Watford boss Javi Gracia does not think Abdoulaye Doucoure's form will be affected by his omission from France's latest squad.