Martinez was trailing 3-0 when he approached the mound to begin warming up for the fourth. The right-hander, who gave up seven hits, three runs and one walk with one strikeout, never got the chance as manager Charlie Manuel brought in Chad Durbin.
Phillies officials waited until the bottom of the sixth inning to announce that the three-time Cy Young Award winner was diagnosed with stiffness in the right side of his neck.
Philadelphia had a 7-0 record in Martinez's seven starts this season. He was coming off a 130-pitch performance that included eight scoreless innings, six hits, no walks and seven strikeouts in a 1-0 victory last Sunday against the New York Mets, his former team.
In a 9-4 victory over Atlanta on Friday, rookie starter J.A. Happ pitched just three innings for the Phillies. The team said Happ left for "precautionary reasons" after he missed his two previous turns in the rotation because of a strained oblique.
Philadelphia signed Martinez to a $1 million, one-year contract on July 15, though the deal was worth an additional $500,000 if he met certain incentives.
Martinez was not offered a contract after going 5-6 with a 5.61 ERA in 20 starts last year for the Mets. After helping Boston win the 2004 World Series, he signed a $53 million contract, but won just 32 games during his stay with New York, missing the playoffs in '06 and undergoing major shoulder surgery that limited him to five starts in '07.