The right-handed throwing McGowan will be opposed by New York's CC Sabathia.
McGowan (0-0) has compiled a 9.00 ERA in two appearances this season for Toronto after not pitching in the majors since July 2008 because of shoulder injuries.
Cecil is listed as day to day and expected to miss only one start because of the injury.
The Blue Jays also activated outfielder Colby Rasmus from the 15-day disabled list.
Rasmus landed on the DL after jamming his right wrist versus Kansas City on August 23. He is batting .216 with three home runs and 12 RBI since joining the Blue Jays in a trade with St. Louis.