The South African had hit out at the International Paralympic Committee (IPC) after last night's race for failing to act over the length of some athletes' blades after Oliveira, wearing noticeably longer ones, came from way back to pip him at the line.
The Brazilian took gold in 21.45secs, leaving Pistorius to settle for silver, coming home in 21.52secs. The 80,000 spectators greeted the result with stunned silence.
In a statement released today, Pistorious said: "I would never want to detract from another athlete's moment of triumph and I want to apologise for the timing of my comments after yesterday's race.
"I do believe there is an issue here and I welcome the opportunity to discuss with the IPC, but 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."
After making his remarks last night, Pistorius sent congratulations to Oliveira on Twitter, the internet social networking site.
Pistorius, who was the reigning T44 200m champion, cannot alter the length of his blades if he wants to continue to compete in able-bodied competition because they have to conform to the International Association of Athletics Federations' regulations.
Pistorius claimed he was not competing on a level playing field, even though the new blades, which are about four inches taller than those used by him, are within the rules.
He said last night: "I've never seen a guy come back from eight metres (behind) on the 100m mark to overtake me on the finish line.
"The guys are just running ridiculous times and they're able to do so.
"We've known (about the longer blades) for about a month. I've brought it up with the IPC, but nothing's been done about it. I believe in the fairness of sport, I believe in running on the right length."
Oliveira hit back, suggesting Pistorius was trying to deflect attention from his defeat.
He said: "He is not a bad loser, he is a great athlete. I am just sad with the interview where he said my blades were too big.
"For me he is a really great idol and to hear that from a great idol is difficult."
The pair are set to go head to head again in the finals of the 100m and 400m on Thursday and Saturday respectively.
A spokesman for the IPC said: "There is a rule regarding the length of the blades, which is determined by a formula based on the height and dynamics of the athlete.
"All athletes were measured today prior to competition by a classifier and all were approved for competition."
The row overshadowed a day when Scottish athletes had hauled in another impressive medal tally.
Glasgow cyclist Aileen McGlynn bagged her second medal of the Games in the women's blind and visually impaired three-kilometres tandem pursuit.
Along with sighted pilot Helen Scott, McGlynn, 39, took bronze after winning silver in the 1km Time Trial on Friday.
They were up against British pair Lora Turnham and her pilot Glasgow-born Fiona Duncan, in the race for third place.
McGlynn, the Evening Times Scots Sportswoman Of The Year in 2009, said: "I'm more happy with this bronze than with my [Sprint] silver because we didn't do any specific training for the Pursuit."
The highlight of the day was the battle between Britain's tandems, made more exciting by the disqualification of favourites Anthony Kappes and Craig MacLean in Saturday's 1km Time Trial, which saw Scot Neil Fachie and Barney Storey take gold.
Fachie, 26, from Aberdeen, said: "We have achieved what we came to do and that was to win two medals."
MacLean and Kappes will still see their faces on special edition gold medal stamps after winning in the Men's B Sprint final.
In the Olympic Arena, Stef Reid leapt into second place to secure a silver medal in the Long Jump.
She jumped a Paralympic record for her F44 class to win silver but was pipped to the gold by Australia's Kelly Cartwright.
There was double disappointment for Reid when she later finished last in the Women's 100m.
On the water, rower David Smith, 34, from Aviemore, won gold in the Mixed Coxed Four – Britain's first rowing medal of the Games.