Garzon, who won fame for his attempt to extradite former Chilean dictator Augusto Pinochet for human rights abuses, stands accused of improperly investigating alleged crimes carried out under the dictatorship of Spain's Francisco Franco.
The decision to put Garzon on trial will lead to the Spanish judges' governing body, the CGPJ, temporarily suspending Garzon from his duties at the high court, the court said. It is still not known when the trial will start.
The proceedings stem from a lawsuit brought against Garzon by the rightist union Manos Limpias, who were later joined by the group Libertad e Identidad and the far-right Falange party, which was powerful during the Civil War but is now marginalised.
Garzon ordered an investigation in October 2008 into the forced disappearance of more than 100,000 people during the 1936-39 civil war and the ensuing dictatorship of Franco, at the request of the victims' families.
Suspects may not be tried in Spain for crimes committed more than 30 years ago. Franco died in 1975, and the crimes under investigation were perpetrated in the 1930s and 1040s.
He later dropped the probe following criticism by state prosecutors, but passed responsibility for exhuming mass graves to regional courts.
This week, the International Criminal Court in The Hague offered Garzon a position as a consultant for seven months to improve its investigative methods. Garzon, who has already assisted the ICC prosecutor in an ongoing preliminary examination in Colombia, had asked for a transfer to work at the ICC, the world's first permanent tribunal set up to try war crimes and crimes against humanity.
"Judge Garzon's extensive experience in investigating massive crimes committed by States and non state organisations will be a great contribution to my office," Moreno-Ocampo said.
Garzon faces two other Spanish Supreme Court enquiries: one for bugging corruption suspects linked to the opposition Popular Party, and another for dropping an investigation into the head of Spain's biggest bank Santander after receiving payments for giving courses sponsored by the bank in New York.
