Adan Mohamed Abidkadir Adan, Mohamed Ahmed Abdi, Liban Abdullah Omar and Hussein Hassan Mustafah all pleaded not guilty to charges of "supporting a terrorist group" on Wednesday.
The men have been accused of supporting the gunmen who carried out the September attack that killed at least 67 people.
In court, witness Stephen Juma described how he had been directing traffic outside the mall when a car pulled up to the building and three men leapt out.
"I began to hear gunshots, I made a radio call for help while running to the main entrance," Juma said. "I took shelter in a residential compound until when I saw policemen come," adding that he had not seen the faces of the three men.
A warning to Kenya
Security forces initially reported that a dozen gunmen carried out the attack, but now it is thought that there were only four gunmen.
Two of the shooters are named in court documents as Mohammed Abdinur Said and Hassan Abdi Dhuhulow, a 23-year-old Somali who spent time in Norway.
It is believed that all attackers were killed in the siege. Interpol and the FBI have assisted Kenya in trying to identify four bodies believed to be those of the attackers. But a New York police report said a lack of evidence could mean the attackers escaped.
Al-Shebab said the gunmen came from a special suicide commando brigade and that the attack was a warning to Kenya to pull its troops out of southern Somalia, where they are fighting the group as part of an African Union force.
Western officials have said that as many as 94 people could have died in total in the mall attack, as bodies were buried under tonnes of rubble after part of the mall's roof collapsed at the end of the raid following an intense fire that burned for weeks.