With Real coasting to victory in Amsterdam and enjoying top spot in Group G, both Spain internationals were shown second yellow cards for blatant time wasting late on.
Ramos and Alonso will now be suspended for the meaningless final group game against Auxerre and their disciplinary records will be wiped clean for the start of the knockout stages.
Suspicion was immediately raised and on Monday morning Madrid-based daily Marca published a series of photographs which suggested coach Jose Mourinho relayed a message to the players via substitute goalkeeper Jerzy Dudek and No. 1 Iker Casillas.
Dutch broadcaster NOS also had footage of Mourinho talking with midfielder Alonso on the touchline prior to his second booking for taking too long over a free-kick. Ramos was dismissed after delaying the taking of a goal-kick.
UEFA has now said it is aware of the incidents and that officials have been instructed to look into the matter.
Article 5.1 of UEFA's regulations - which deals with loyalty, integrity and sportsmanship - dictates that both players could have their suspensions extended if found guilty of an offence.
Mourinho said on Tuesday night: "I spoke with many players throughout the game, not only with Ramos and Alonso. The two red cards were the result of strange referee bookings in an easy game to monitor.
"I didn't like them one bit, but if Ramos or Alonso can't face Auxerre others will take their place. We will not give our game against the French away. We want to win all our matches."