Girardi had come to the mound to remove CC Sabathia after the left-hander served up a three-run homer to Adrian Gonzalez in the seventh inning, opening up a 6-0 lead for Boston.
After signaling in Dave Robertson from the bullpen, Girardi and Winters began an exchange that grew heated, as Girardi moved close to Winters' face while yelling.
Girardi had appeared to have been irked by a Sabathia pitch to Jason Varitek that was not ruled a strike. Varitek hit an RBI single to continue the inning and was on base when Gonzalez homered.
Following the ejection, Girardi kicked dirt toward the backstop behind home plate, but not at Winters. Bench coach Tony Pena assumed control of the club in Girardi's absence.