Just before the US Grand Prix Ferrari confirmed they had deliberately broken a seal on Felipe Massa's car, incurring a five-place grid penalty.
Massa dropped to 11th, which moved Fernando Alonso from eighth to seventh and onto the clean side of the grid.
It proved successful as Alonso finished third and lost only three points to runner-up Sebastian Vettel of Red Bull, with McLaren's Lewis Hamilton claiming victory.
It means the title race goes down to the wire in Sao Paulo on Sunday, with Alonso 13 points adrift of Vettel.
Asked whether he would have done the same, Whitmarsh said: "I don't think so.
"Team principals decide how to run their programmes, and it is very clear they are focused on Fernando.
"I'm not criticising anyone. You have to go racing as you see fit," he said.
"If I had qualified on the right-hand side of the grid, but then I was moved on to the slow side, I would have been very pissed off."
Ferrari principal Stefano Domenicali insisted: "It was the right thing to do, and I have to thank Felipe for his help."