Bay, who spent six weeks on the DL due to a rib fracture, was not in the lineup for the Mets' game against the Washington Nationals.
Manager Terry Collins said Bay had been sick for a few days and he planned to play him on Thursday.
Bay played left field on Tuesday night for Class-A St. Lucie in the second game of a rehabilitation assignment.
"From what I've been told, and from what I feel, it feels completely healed," Bay said. "I was prepared to play, but at the same time I think at this point one more day's not gonna kill me."
New York also placed right-handed pitcher Chris Young, who started Tuesday's game, on the paternity list. It was Young's first start in more than a year after shoulder surgery.
Collins said that infielder Ruben Tejada, who's on the disabled list with a strained right quad, returned to New York for an examination after he removed himself from a rehab start in Buffalo on Tuesday.
He also said that Jon Rauch who won't pitch in the series against Washington with debris in his elbow may be placed on the DL if he's not ready to pitch on Friday against the Yankees.