About 40 minutes before the first pitch on Monday afternoon at Citizens Bank Park, the Marlins scratched Stanton due to left knee pain.
Manager Ozzie Guillen said Stanton will be examined by a physician in Philadelphia.
"It's something different than what he had in the spring," Guillen said.
Stanton had inflammation in the knee in Spring Training, and the pain he felt on Monday is in a different area. With an off-day on Tuesday, Stanton will get back-to-back days of rest. The team lists the 22-year-old right fielder as day to day.
Guillen didn't rule out Stanton being available on Wednesday in the second of three games at Citizens Bank Park.
Stanton, Miami's cleanup hitter, is off to a 4-for-17 (.235) start with a double and three RBIs. His left knee bothered him last year.
Austin Kearns replaced Stanton in right field in the series opener with the Phillies. Kearns originally was slated to start in left field, as Logan Morrison was given the day off. Chris Coghlan made the start in left field. Kearns homered in the ninth inning Monday off Philadelphia closer Jonathan Papelbon.
Stanton and Morrison both missed substantial time in Spring Training due to knee ailments. Morrison had surgery on his right knee in early December. The team is keeping a close watch on Morrison, who was given Monday, as well as last Thursday, off.
With temperatures in the upper 50s in Philadelphia, the Marlins aren't taking any chances with their young corner outfielders.