Pistorius streaked into an early lead and was almost 10 metres ahead as the athletes came into the home straight but the Brazilian launched a stunning fightback and surged to victory over the final few metres.
The result left the South African double amputee, who was defending his 100m, 200m and 400m Paralympic titles from Beijing, seething and he claimed his opponent's prosthetic blades were too long.
In a statement on Monday, the sprinter stuck to his claim but apologised for raising his concerns immediately after.
"I want to apologise for the timing of my comments but I do believe that there is an issue here," said the 25-year-old, who last month became the first double amputee to run in the Olympics and made the 400 metres semi-finals.
"I accept that raising these concerns immediately as I stepped off the track was wrong.
"That was Alan's moment and I would like to put on record the respect I have for him.
"I am a proud Paralympian and believe in the fairness of sport. I am happy to work with the IPC (International Paralympic Committee) who obviously share these aims."
His original comments after Sunday's race, made to Channel 4, were: "This is a really strong race of mine, and as I said in the mixed zone, the size of some of the other guys' legs are unbelievably long.
"Not taking anything away from Alan, he's a great athlete, but the guys who do the measuring in the courtrooms, some of these guys are a lot taller and you can't compete for stride length.
"We're not racing a fair race. The International Paralympic Committee have the regulations, but the regulations allow the athletes to make themselves unbelievably high. We tried to address the issue in the weeks leading up to this, but it fell on deaf ears.
"The guys are running ridiculous times. Alan is a great athlete, but I run just over 10 metres per second, so I don't know how you can come back from eight metres behind after 100m to win. It's ridiculous."
Oliveira's winning time was still 0.15 seconds slower than the world record set by Pistorius in Saturday's heat.
"He is a really great idol, and to listen to that coming from a really great athlete is really difficult," Oliveira said on Sunday night. "I don't know who he's picking a fight with - it's not with me.
"The length of my blades are all right because I went through all the procedures with the referees.
"Once I came inside the track, it had all been cleared up and I think Pistorius also knows that.
"I have been using them for a whole month; just the same blades, according to the IPC rules...
"I am very happy: I have written my story on the Paralympic wall."