Former MK member Ernest Sigasa, who headed the ANC guerilla army's Johannes Nkosi unit, told the TRC amnesty committee his unit monitored the restaurant for some time before placing a limpet mine there.
A civilian was killed and 66 people injured in the Saturday afternoon attack in July 1988.
Among the 80-odd people who attended the hearing in the Benoni town hall on Monday was Vic Serrano, whose daughter Marryanne was killed in the blast.
Safety and Security Minister Sydney Mufamadi attended the hearing to give moral support to the MK members.
A small group of Freedom Front Youth members displayed graphic photographs of the damage caused by the explosion.
Sigasa said it was regrettable that innocent people died during the attack, but he did not regret executing an act aimed at security personnel.
"It was not ANC policy to target innocent civilians but we targeted Wimpy because the top brass from the Benoni police and their counterparts frequented the place. People who were inflicting terror on our activists in prison were the first target.
"Civilian casualties were inevitable, and where life is lost - whether black or white - it is a shame," Sigasa said.
Sigasa said fellow amnesty applicant Elfus Ndlovhu monitored the Wimpy outlet and kept information about police and security branch members who dined and held meetings there.
The MK unit would meet every Wednesday to assess information gathered about the Wimpy meetings.
Sigasa, who is now a businessman, said while he had not planted the limpet mine he was party to the decision to do so.
Another applicant, Tebogo Kebothlale, now a senior North West government employee, said in his brief testimony he agreed with everything his commander, Sigasa, told the commission. Kebothlale is also applying for amnesty for the bombing of the Katlehong railway line, attacks on police barracks and councillors' homes, the ambushing of a police constable, and attacking a whites-only bus terminus.
The hearing continues.