Rauner did not give a reason for denying clemency.
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Perez is a green card holder and army veteran. He was taken into custody by ICE after he served seven and a half years in prison for a non-violent drug charge.
Perez and his family had hoped that a pardon from Rauner would put him on the path to citizenship.
"It's not appropriate to go into detail on reason for a decision, but we take every review of clemency and pardon very seriously," Rauner said. "We made the decision not to grant it in that case."
Perez's mother, Esperanza Perez, expressed disbelief at the decision.
"It's not fair because my son is a hero, he is not a criminal," Esperanza Perez said.
Perez served two tours of duty with special forces in Afghanistan.
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On a phone call from jail, Perez said he thought Rauner's support for veterans would help his cause.
"I was sad, I was upset and heartbroken," Perez said. "I really believed he would grant me a pardon because of the way he's been talking all along"
Perez said his case is a veteran's issue, not an immigration issue. He said he has not given up hope, especially after Illinois Senator Tammy Duckworth introduced Thursday a private bill that would give Perez citizenship.
However, Duckworth's bill is considered a long shot.
"If she can get the right people in leadership to request a report, it would automatically stay any kind of deportation," said Chris Bergin, Perez's attorney.
Perez is awaiting deportation in a Kenosha detention center and is in the seventh day of a hunger strike to protest the decision. He said he has not been to Mexico since he was eight years old and fears for his safety if he is deported.