"I saw nothing wrong with what occurred," the former Monaco winner and ex-team owner told BBC radio.
The International Automobile Federation (FIA) has said it is looking into "incidents" involving the championship leaders "in light of a possible breach of the International Sporting Code."
The controversy concerns so-called "team orders", banned after the 2002 Austrian Grand Prix where Ferrari told Brazilian Rubens Barrichello to let Michael Schumacher win.
Double world champion Fernando Alonso won for McLaren on Sunday, ahead of British rookie team mate Lewis Hamilton. The two are now level on 38 points but Spaniard Alonso leads the championship on race wins.
Hamilton, who finished runner-up for the fourth race in a row, said he had been told to ease off to ensure the one-two outcome.
McLaren have said they simply had a strategy to win the race.
"I make no excuses for instructing the racing drivers to slow their pace after the first stop and to effect our strategy," team boss Ron Dennis said on Sunday.
Stewart said: "The Schumacher-Barrichello case was blatant. He reduced his speed by maybe 30 or 40mph to have Schumacher pass him before the finishing line," said Stewart.
But it's a very difficult thing to start telling team owners that if you are running first and second that you should keep driving your drivers to the absolute limit of their ability.
"What if he (Hamilton) had tried a little bit too hard in these last laps in Monaco and slid off the race track, hit a barrier and taken the McLaren out of the race?," he added.
Bookmakers Williams Hill have suspended all betting on the outcome of the championship pending the investigation while Paddy Power said they were refunding bets on Hamilton.
"It's hard enough to pick a winner even when your selection is actually trying to win. The only fair thing to do is give punters their money back," declared the Paddy Power Web site (www.paddypower.com)