Nani was red carded after 56 minutes of United's last-16 second leg tie with Real Madrid at Old Trafford on Tuesday evening, after colliding with visiting full-back Alvaro Arbeloa.
Referee Cuneyt Cakir deemed the Portuguese winger's high boot as dangerous and gave him his marching orders, and United subsequently saw their 1-0 goal lead on the night turn into a 2-1 defeat and slipped out of Europe's premier club competition 3-2 on aggregate.
Red Devils boss Sir Alex Ferguson refused to attend the post-match press conference, with his assistant, Mike Phelan, saying the Scot was 'distraught', and former Celtic and Aston Villa striker McInally told Sky Sports HD that he could understand the 71-year-old's frustrations.
"[Nani's sending off] was a shocking decision that has put Man United out of the Champions League," said McInally. "I've been on the end of some of Ferguson's blasts but I cannot think how angry he is at the moment because United were there.
"The referee must have thought Nani's challenge was over-aggressive, dangerous or that he had kicked out, but Nani is a good enough player to think he can control the ball and bring it down.
"There is no way he sees Arbeloa coming in - he would have needed to have eyes like an iguana to see him - so it's an absolute disgrace; the referee didn't have many decisions to make in the game but he got that completely wrong.
"And from that moment on Real were like: 'We have a real chance here' and they pinned United back. It was like the Alamo, and you thought: 'This could end up being four'."
Erstwhile Liverpool midfielder Dietmar Hamann, who joined McInally in the Sky Sports studio, also felt that Nani's dismissal was harsh, but he praised the way Real Madrid battled from behind to prevail.
The German hailed the impact of ex-Tottenham midfielder Luka Modric, too, who emerged from the substitutes' bench to fire Los Blancos level, and says Jose Mourinho's men will be a hard side to stop in April's quarter-finals.
"Not one Real Madrid player surrounded the referee when Nani was sent off and as the United player didn't mean (to make contact with Arbeloa), I don't think it's a foul, let alone a booking or a sending off," said Hamann.
"Before the red card, Real had the ball but were struggling to create chances, just like at the Bernabeu, and if it had stayed 11 versus 11 you had the feeling United were going to go through, but after the sending off Real were electric.
"They penned United back into their own half, created chance after chance and scored two really good goals - and Modric, who has had a tough time in Madrid, changed the game and his finish was fantastic.
"Man United had chances and (Real goalkeeper) Diego Lopez made some good saves - although he probably made more of a couple of them than he needed to! - but Real could have got a third, too, and showed what a great team they are.
"They have so much firepower and when Iker Casillas comes back in goal it will make them even stronger. They look like a team on a mission - and I wouldn't like to face Real in the last eight."