Lester Dumakude, 45, now a lieutenant-colonel in the SA National Defence Force, told the Truth and Reconciliation Commission's amnesty committee hearing in Johannesburg that he thought the two victims were security guards employed at Ellis Park.
Clive Clucas, 48, and Linus Marais, 34, who had just left the stadium after watching a Currie Cup rugby match between Transvaal and Free State, were killed instantly when the bomb exploded near them.
Dumakude said he took over command of the special MK operations unit in 1987 from Aboobaker Ismael, who has applied for amnesty for among others the 1983 Church Street car bomb which killed 19 people and injured more than 200.
Dumakude has applied for amnesty for all acts committed by units under his command since 1981.
He said in his application the MK special operations unit he commanded was granted a broad mandate to carry out attacks and to report back afterwards.
Dumakude said he considered himself an explosives expert as he was trained in the use of explosives in Cuba and the former Soviet Union.
He assembled the Ellis Park bomb and personally detonated it using a remote control device on July 2, 1988.
The unit consisted of three other MK operatives, Harold Matshididi, 51, Aggie Shoke, 44, and Itumeleng Dube, who was supposed to appear before the committee on Tuesday but could not be traced.
Dumakude on Tuesday said he was watching the car in which he placed the bomb when he saw Clucas and Marais approaching him. The bomb had been primed and the car parked near Ellis Park on the day of the rugby match.
"My actions attracted their attention. To me they looked as if they were part of the security in the area," Dumakude said.
The two men then turned away from him and walked back in the direction of the car when he detonated the bomb using the remote control device, killing both men instantly.
He said it was never the intention of the unit to kill any civilian targets. The device was set to explode before the end of the rugby match, before the crowd emerged from the stadium.
"I did, however, foresee the possibility that civilians could be killed. It sometimes happen that people leave the match before the end of the game.
"It was for that reason that I used three seperate detonating devices to allow me to react to the situation as it unfolded."
Dumakude said a clock was wired to the bomb to detonate it at 5pm, but he also had a remote control trigger device in case the match ended earlier.
"Those who died in the explosion were the people who made me trigger the device," Dumakude said.
He denied he triggered the bomb because he was scared the two men might discover it. He said he did it to prevent greater loss of life.
He said he was faced with the choice of either detonating the bomb in the presence of the two men, or to wait for the timing device to trigger the bomb later and kill more civilians.
TRC evidence leader Paddy Prior asked Dumakude if it was his intention to kill the two men he believed were security guards.
"No it was not my intention," Dumakude said.
Prior put it to him there was no reason to believe the two men were security guards. "You are not telling us exactly what happened there," Prior said.
Asked by committee chairman Judge Andrew Wilson why he did not set the bomb to go of much earlier, but instead waited for the crucial moment when people started leaving, Dumakude said he did not want to "disturb the match".
"You plant a massive bomb to send a message to the white people, but you do not want to disturb a rugby match?" Wilson asked.
Dumakude said Ellis Park was chosen as a target because it would bring the struggle closer to the white community.
Earlier on Tuesday Clive Clucas' wife Sally said she would and could not forgive her husband's murderers.
Clucas, her daughter Joanne May Staples and her son Ken Clucas, are opposing amnesty for the bombers.
Marais' wife Magriet Erasmus said she and her two daughters, aged three and six, ms since her husband's death.
She said her daughters did not want to attend the proceedings as they were not willing to face their father's killers.
Erasmus said she did not believe the applicants had divulged the whole truth about what happened that day.
The hearing continues on Wednesday.