Halladay walked two of the first three batters he faced before leaving after a long discussion with manager Ryne Sandberg. He was replaced by Luis Garcia.
The 36-year-old two-time Cy Young Award winner had surgery on his right shoulder on May 15 and returned to the mound on Aug. 25.
He came into the game with a 4-4 record and 6.71 ERA in 12 starts.
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