Rooney, who played as a lone striker for an hour in Istanbul, shook his head as he came off before furiously throwing down his boot after removing it in the dug-out.
"He is never pleased to come off. He has so much energy he wants to play all the time," said Ferguson. "He had been playing as the lone striker for an hour, which is why he was always going to come off. It was always part of our thoughts to bring Wayne off."
Given the work he had to do for England in two internationals, and a gruelling examination at Tottenham, when he was part of a side that completed the game with only 10 men, Rooney might have been glad of the break, particularly as Manchester City go to Old Trafford on Sunday.
But instead Rooney was clearly put out and his obvious anger at being substituted also led to him being goaded by Besiktas supporters behind the dug-out, with whom he exchanged a brief word, and the arrival of security men.
Meanwhile, Police were forced to intervene to get a group of Besiktas fans away from the visitors' dug-out, while Ferguson confirmed Jonny Evans had been targeted by a supporter carrying a laser.
"It was in the first-half, although thankfully the police did something about it," said the United boss. "They managed to get the culprit, which is good because I noticed it particularly on Jonny Evans. It seemed to be on him all the time."
Ferguson was also altered to a security problem behind his dug-out, although he was eager not to make an issue of that.
"Someone mentioned it to me, but I never saw anything," he said. "I do know the fans made the loudest noise I have ever heard. They never stopped the whole night."
It didn't stop United opening their quest to reach a third successive Champions League final in the perfect manner. Paul Scholes, who is suspended for the Manchester derby, eventually scored United's winning goal in the 77th minute.
Ferguson was delighted with his team's overall display, particularly Antonio Valencia, who was making his Champions League debut following his £17 million summer arrival from Wigan Athletic.
"Antonio was always a threat," said Ferguson. "He got to the by-line so many times and really we should have done better.
"He has got the potential to be a really good player. He is powerful and strong, with a lot of enthusiasm. He is very quick, with good balance and in a years' time he will have developed more parts of his game."