Webb, who has been out since Opening Day with a shoulder injury, had been playing catch on the side and throwing bullpen sessions on flat ground. Friday was supposed to be his first session off the mound since he suffered a setback in April.
Webb was seen leaving Kauffman Stadium prior to Thursday night's game.
When asked about it, D-backs GM Josh Byrnes said Webb "didn't feel good."
"We decided to cancel the bullpen session [Friday]," Byrnes said. "He is heading back to Phoenix."
Said D-backs manager A.J. Hinch, "He was sore and he went back to Phoenix. We'll reevaluate [Friday]. He didn't feel very good today. So it's a bad sign for us. We were so positive about where he was in his rehabilitation. He'll have to get further tests and see our doctors."
Steve Gilbert is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.