Judge Miguel Angel Galvez granted prosecutors' request to try Perez on charges of customs fraud, racketeering and bribery, and remanded the fallen conservative leader in custody.
The judge gave the prosecution three months to continue its investigation, after which the 64-year-old retired general will face trial.
"I don't understand why I've been charged," a visibly distraught Perez told journalists as police escorted him from the court.
"There's not a single piece of evidence," he said. "I'm sure I have never participated in any criminal network."
His next court date was set for December 21.
Prosecutors and investigators from a UN commission tasked with fighting high-level graft in Guatemala accuse Perez of orchestrating a scheme in which businesses bribed corrupt officials to clear their imports through customs at a fraction of the actual tax rate.
They say the accusations are based on some 89,000
The scheme -- dubbed "La Linea" (the line), for a hotline businesses allegedly called to access a network of corrupt officials -- collected $3.8 million in bribes between May 2014 and April 2015, including $800,000 each to Perez and jailed ex-vice president Roxana Baldetti, prosecutors allege.
Perez denies the charges.
The conservative leader defied months of mass protests calling on him to quit, but was left with little choice after Congress stripped him of his immunity and a judge issued a warrant for his arrest last week.
He resigned Wednesday night and was jailed Thursday after an initial court appearance.
Guatemala
Comedian and political novice Jimmy Morales won the presidential race, but fell well short of the 50 percent needed to avoid a runoff.
He will face either former first lady Sandra Torres or millionaire businessman Manuel Baldizon in a second-round vote on October 25.
Newly sworn-in President Alejandro Maldonado, a former Constitutional Court judge, will serve out the remainder of Perez's term, which ends on January 14.
