Howard missed Saturday's 64-51 loss to Miami due to the same illness, which he prefers to keep private.
"I just have to take a step back and give myself a chance to get better," Howard told Waters.
The Syracuse trainers have identified the illness, and have determined it is not contagious.
The freshman guard is averaging 1.7 points, 1.6 rebounds and 1.5 assists per game this season. He has appeared in eleven of SU's fifteen games. Howard scored a season-high six points against Texas Southern on December 27th, where he played a season-high 19 minutes.
Syracuse (10-5, 0-2) will host Clemson (8-6, 1-1) on Tuesday night at 8 p.m. ET at the Carrier Dome.