Alonso and Ramos both collected second cautions for timewasting late in Real's 4-0 win at the Amsterdam Arena on Tuesday.
They will serve one-match suspensions in a meaningless final group match against Auxerre, then could start the knockout rounds in February with a clean disciplinary slate.
Uefa says its disciplinary unit will look at the incidents.
Dutch broadcaster NOS showed footage of Madrid coach José Mourinho speaking to Alonso on the sideline before he picked up his second yellow. However Mourinho later dismissed any suggestion he had instructed his players to seek deliberate punishments.
Mourinho said: "I spoke with many players throughout the game, not only with Ramos and Alonso.
"Stories sell, but the important thing is the 4-0 win and the fantastic game we had. Let's talk about that and not other things.
"The sendings-off came after an easy game where the referee has shown some strange yellows.
"They are cards that I don't like. It was an easy game to control. Ajax made a lot of fouls and in the first from Ramos he was shown a yellow card."
Mourinho admitted it did not matter that Alonso and Ramos would miss their final group game, but insisted he still wanted to beat Auxerre at the Bernabéu in December.
"The red cards we picked up don't matter hugely as we have already qualified ahead of the next game against Auxerre. If Ramos and Alonso can't play against Auxerre then there will be others, but we are not going to gift the game to the French. We want to win them all."
Right. I think many more double yellows should be looked at before they get punished for something like this. Pique.