The South African had criticised the International Paralympic Committee, saying gold medallist Alan Oliveira's artificial legs were too long.
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."
The world record holder was overhauled by Oliveira in the final 20m of the race, won by the Brazilian in 21.45 seconds with Pistorius second in 21.52.
The IPC said all artificial legs - known as blades - adhered to strict regulations and had been verified and agreed before the race.
But immediately after his loss, Pistorius told Channel 4: "We are not running in a fair race here.
"I don't know how you can come back, watching the replay, from eight metres behind on the 100 to win. It's absolutely ridiculous."
Oliveira said the comments of his "idol" were hard to take.
"The length of my blades is all right," said the South American. "I went through all the procedures with the referees. I believe Pistorius also knows that."
Pistorius set a new world record of 21.30 seconds when qualifying for the final on Saturday, breaking the mark of 21.88 set by Oliveira in his own heat two races earlier.
On Monday morning Pistorius issued the apology.
"I accept that raising these concerns immediately as I stepped off the track was wrong," said Pistorius.
"I am a proud Paralympian and believe in the fairness of sport. I am happy to work with the IPC who obviously share these aims."
IPC communications director Craig Spence said Pistorius had raised his concern over the rules with them.
"We agreed to meet him at a later date so he could he raise his questions in a formal environment away from the emotion of the stadium," Spence said.
"The IPC respects the significant role Oscar has played in raising the global profile of Paralympic Sport since his Games debut in 2004. Therefore we are more than willing to give him an opportunity to air his views in a non-emotional environment at a meeting to be organised at a later date."
The IPC said in a statement that all competitors had been checked before the race.
"All were within the regulations outlined in the IPC Athletics Classification Handbook," the IPC said.
"Since 2010 athletes competing at IPC international competitions have been checked at regular occasions in the call room prior to participation."