The men, and two others whose committal hearings will continue this month, are all charged with belonging to a terrorist group.
Several also are charged with funding or providing support to a terrorist organisation or possessing something connected with a terrorist act.
Their alleged leader, Islamic cleric Abdul Nacer Benbrika, 46, of suburban Dallas, also is charged with directing the activities of the alleged terror cell and recruiting for the group.
After a six-week hearing, Magistrate Paul Smith said today there was enough evidence for convictions to be possible.
"I am satisfied in relation to all defendants except Mr Joud and Mr Kent that there is sufficient evidence upon which a jury could convict," he said.
The men sat calmly behind glass barriers in segregated docks as Mr Smith announced his decision.
Seven of them refused to stand when directed to by Mr Smith, but the magistrate continued to read their charges and ask for their pleas.
Police say the 13 men were in the early stages of carrying out a terrorist act when 10 of them were arrested in pre-dawn raids in Melbourne and Sydney last November.
The other three were arrested in March this year.
Two year investigation
The arrests were part of a two-year counter terrorism investigation called Operation Pendennis.
An undercover police agent had infiltrated the group and discussed details of blowing up buildings with Benbrika, the court was told.
The officer, known as "security operative 39", had accompanied Benbrika to north-eastern Victoria to witness a trial explosion, Prosecutor Mark Dean SC said.
Mr Dean said the group was inspired and influenced strongly by the terrorist group al-Qaeda and the teachings of its leader Osama
bin Laden.
All 11 men committed to stand trial pleaded not guilty today.
They are Benbrika, Fadal Sayadi, 26, of Coburg, Majed Raad, 22, of Coburg, Ahmed Raad, 23, of Fawkner, Bassam Raad, 24, of Brunswick, Ezzit Raad, 24, of Preston, Amer Haddara, 26, of Yarraville, Abdullah Merhi, 21, of Fawkner, Hany Taha, 31, of Hadfield, Shoue Hammoud, 26, of Hadfield and Izzydeen Atik, 26, of Williamstown.
Outside court, Merhi's brother Omar Merhi said the men were innocent and the case was "a trophy trial".
He said his brother had been locked in solitary confinement for 300 days.
"The Howard government and (Attorney-General) Philip Ruddock have a lot to answer for," he said.
Mr Smith ordered the 11 men to face a directions hearing in the Victorian Supreme Court on December 1.
Several of the men will apply for bail in coming weeks, their lawyers told the court.
The committal proceedings for Shan Kent, 29, of Meadow Heights, and Aimen Joud, 21, of Hoppers Crossing, will resume on September 18 in Melbourne Magistrates' Court.