According to Mets general manager Sandy Alderson, the left-hander allowed one hit and struck out four.
Santana made a start for Savannah in the first round of the Class A South Atlantic League playoffs, but he decided not to pitch on Thursday in the championship round against Greensboro.
Santana may pitch in his native Venezuela this winter if he feels up to it and believes it will help him be ready for Spring Training. The Mets remain confident that the two-time American League Cy Young Award winner will be ready to go next season.
Santana was 11-9 with a 2.98 ERA in 29 starts in 2010 prior to September shoulder surgery and has two years and $55 million remaining on the six-year, $137.5 million contract he signed in 2008.
The initial estimates pegged his return to the Mets for June or July this year, but various setbacks stalled his rehab throughout the summer.
Jonathon Niese, on the disabled list since late August with a rib cage injury, will also not make it back this season. The left-hander is 11-11 with a 4.40 ERA.