William Little, who was the department's regional representative at the time, said his carreer had been "shattered" by the incident.
Little was the first person to testify in the commission's Western Cape hearings, which opened on Monday at the Nico Malan Nurses Training College in Heideveld, Cape Town.
The bomb attack was allegedly carried out by the African National Congress and was one of several which rocked the Durban area at the time.
"It was a normal working day... At about 5.15pm nature called," Little said in reply to questions by commission deputy chairperson Dr Alex Boraine.
Little said he had remained in the office after hours to complete an urgent affidavit for the police concerning a school fraud case.
Little said he had his own toilet between the second and third floors of the building, which housed mostly office workers.
He remembered finishing in the toilet, but nothing of what happened directly after.
When he came to he was outside the building, in West Street.
"I was hoping to wake up. This was not real. This was a nightmare," Little said, adding he only realised a bomb had exploded when he returned to the scene, which had already been cordoned off by police.
When he returned to his office he was told by a police officer that they were looking for a man who had reportedly been "shouting for help from the second floor".
The staircase to the offices - which he believed he had used to leave the building - and the offices were completely destroyed.
Glass was strewn all over his desk.
If nature had not called, he would have been "killed or severely injured" by the flying glass.
Little had only consulted a doctor the following week when the department's director-general visited Durban and suggested he seek medical attention.
He was then diagnosed as being severely depressed and suffering from anxiety and had received psychiatric treatment.
The director-general had arranged a transfer for him back to Cape Town to be with his family. There he held a clerical post in the department's education offices.
Little said his senior position in Natal had been "high profile", while he was "just left alone" in the clerical post in Cape Town.
"Yes, it affected my carreer," he said.
He did not know whether anyone had been arrested or charged for the bombing.