The South African had called for tougher regulations on running blades after Oliveira, wearing noticeably longer ones, took his T44 200m title.
The Brazilian was way down at the 100m mark, with Pistorius seemingly all but home and dry, but surged through to win in 21.45 seconds.
Pistorius, the original Blade Runner, had to settle for silver. The 25-year-old cannot alter the length of his blades if he wants to continue to compete in able-bodied competition because they have to conform to IAAF regulations.
And he 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 Pistorius, are within the rules.
Hours after his complaint, however, and with his opponent suggesting he was a bad loser, Pistorius apologised for the timing of his comments.
In a statement he said: "That was Alan's moment and I would like to put on record the respect I have for him.
"I want to apologise for the timing of my comments but I do believe there is an issue here."
Earlier, the South African had said: "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."
The Brazilian hit back at Pistorius, suggesting he was trying to deflect attention away 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.
"He was bothered by my time in the semi-finals and he wanted to get to me with his polemic but it did not work.
"For me he is a really great idol and to hear that from a great idol is difficult."
The pair are on course to go head to head again in the finals of the 100m and 400m on Thursday and Saturday respectively.
Pistorius has already admitted he does not fancy his chances over the shorter distance, but the 400m is his main event - he reached the Olympic semi-finals last month - and defeat there would escalate the row even further.
A spokesman for the IPC said: "There is a rule in place 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."
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