The 38-year-old claimed the winger did not deserve the red card shown him by Turkish referee Cuneyt Cakir for a foot-up challenge on Alvaro Arbeloa in the Red Devils' 2-1 loss to Real Madrid, which sealed a 3-2 aggregate defeat.
He wrote on social networking site Twitter: "Been going to OT since age of 5 and I've never seen the whole ground as in disbelief as they were last night at a decision! Nani is a player who regularly tries to control a pass like this over his shoulder and its never a red card! Changed the whole game!Poor ref.
He went on: "The crowd actually weren't angry / weren't shouting they were just open mouthed and in shock!"
Neville felt that if Nani deserved red then so did Madrid goalkeeper Diego Lopez for making contact with Nemanja Vidic when the United defender got his head to a corner ahead of the keeper.
"The Madrid keeper on Vidic looked a similar type of incident," Neville added. "Anyway it won't be the first time or last! Just ruined a fascinating match and didn't feel right to Utd or Madrid people in the stadium!"
Lou Macari, the former United midfielder, branded Cakir's performance "rubbish". "I thought it was a strange decision - a referee from Turkey who we hadn't heard of. He had no great reputation of being one of the top referees," he told BBC Radio Five.
When it was pointed out that Cakir was well regarded in Europe, he said: "He's still rubbish.
"You don't have referees like that for these big games. The referee's assessor was there last night and he's a proper referee from the past, (Pierluigi) Collina.
"I am sure he looked at the decision and thought, 'he's got it wrong'. I couldn't believe it when he pulled out the red card - it was simply a wrong decision."