Kondogbia was suspended for Thursday's second leg, which Valencia won 1-0 to advance to the last 16 via a 3-0 aggregate scoreline.
"The UEFA Control, Ethics and Disciplinary Body has decided to suspend the Valencia CF player Geoffrey Kondogbia for two UEFA competition matches for which he would be otherwise eligible for clearly receiving a yellow card on purpose," a statement read.
Kondogbia will now miss both legs of his side's last-16 tie against FC Krasnodar.
With a precedent set, Real Madrid and Ramos will be left sweating over a potentially similar punishment for the defender.
"Looking at the result, I'd be lying if I said I didn't force [the booking]," he told reporters after the game.
"It is not to underestimate the opponent nor to think that the series is over, but in football you have to make tough decisions."
The following day UEFA announced that they had opened an investigation into the veteran centre-back.
Ramos later backtracked from his comments with a post on social media.
"I want to make it clear that it hurts more than anyone, I have not forced the card, as I did not against Roma in my previous Champions League match," the Madrid captain wrote on Twitter.
"I will support from the stands as one more fan with the illusion of being in the quarters."
However, it appears the damage could already be done, and Ramos could be facing a ban for one or both legs of the Champions League quarter-final should Madrid advance past Ajax.
The Blancos take on the Dutch side at the Santiago Bernabeu on March 5, carrying a 2-1 advantage from the first leg.