The widow of Col Craig Duli, who once served as Holomisa's second-in- command on Transkei's ruling military council, told the commission that Duli was shot in the back of the head at Ncise army base outside Umtata.
She said the execution was witnessed by former Transkei deputy commissioner Lt-Gen Wildon Mbulawa, who was assassinated outside his home in Umtata in 1994.
The commission also heard startling new claims that Holomisa's private secretary, Major Mbulelo Xaba, and senior Transkei Defence Force officers, including TDF chief Gen T T Matanzima, were among the coup plotters.
When Holomisa was appointed Deputy Minister of Environmental Affairs after the 1994 general election, Xaba stayed on as his administrative secretary. Matanzima is currently head of Eastern Province Command.
Sabelo Wana, who was convicted in the Umtata Supreme Court for his role in the coup, told the commission on Wednesday that Matanzima had given Duli the assurance his coup assault force would meet no resistance from the TDF.
Duli intended to replace Holomisa and his military council with an interim structure headed by Transkei's chief justice and nine traditional leaders, including former Transkei president Kaiser Matanzima, Wana said.
"He said we are not going to fight, we are just going to take Holomisa out. He told us we would not meet with any resistance," Wana said. "However, we were betrayed at the eleventh hour by members of the TDF."
After attacking Ncise base with mortars and automatic rifles, Duli, Wana and Boetie Davies, a senior member of Matanzima's bodyguard, managed to force their way into Holomisa's office in the Botha Sigcau government building in central Umtata.
In an ensuing gunbattle with forces loyal to Holomisa, Davies was killed and Duli was wounded in the right thigh by a bullet and in the left eye by mortar shrapnel.
Wana said he and Duli then surrendered and were escorted out of the building. Duli was limping slightly but otherwise appeared uninjured.
The military council claimed later that Duli died of his injuries.
Duli's widow Nontobeko testified that she had met Mbulawa, then head of the Umtata murder and robbery unit, after her husband's death.
He told her he had witnessed Duli's execution by a junior officer at Ncise base as he pleaded for his life.
"He said it was painful what he saw in the camp. Apparently when he (Duli) went to the camp he was only slightly injured. He was told to look this way. That is how he was shot. That was the end of him.
"I felt my husband should have been taken to the courts of law so that he could defend himself."
She asked the commission to probe the circumstances surrounding his death and to find his killers, adding that she held Holomisa's military council politically responsible for the killing.
In 1992, two years after the coup bid, Holomisa had come to her house and had told her he never wanted Duli to die as he had helped to free Holomisa from prison when he was detained in 1987.
"He said if I had any problems I should come to his office. I never asked him what had happened to Craig."
She also told the commission of the close friendship which Duli and Holomisa had shared after Stella Sigcau's government was overthrown and the military council was set up in 1987.
However, in April 1989, their relationship soured and Duli was suspended from the council and jailed for eight months without trial.
Nontobeko said it was alleged her husband had been involved with a group advocating the return to civilian rule.
After his release from prison, he fled Transkei to Aliwal North where he met businessman Vuli Mbotoli, who was later implicated in the coup attempt.
Duli said she had found documents among her husband's clothes after his death, one of which detailed the reasons for the overthrow of Sigcau's government.
She said she was prepared to hand these to the commission.