Fernandez will sit out the FA Cup quarter-final against Port Vale on Saturday and the EPL match with Manchester City next weekend, Chelsea coach Liam Rosenior confirmed on Friday.
The sanction was in response to Fernandez telling a podcast this week that he would like to live in Madrid. That fuels speculation linking him with a move to Real Madrid even though he' is contracted to Chelsea to 2031.
Fernandez's agent Javier Pastore said the Argentina international does not understand the decision.
"The punishment is completely unfair," Pastore told The Athletic. "Banning the player for two matches, which moreover are also absolutely crucial for Chelsea because qualification for the Champions League is at stake and he is one of the team's most important players.
"There's no real reason or justification for why he has been banned. Enzo didn't understand the situation. When the coach told him he accepted it because he's a highly professional guy who's always fully committed wherever he is and respects decisions.
"But we don't understand the punishment because he doesn't mention any club or say he wants to leave Chelsea, far from it. He only mentions Madrid, the city.
"Our plan after the World Cup is to meet with Chelsea again and, if there is no agreement, to explore other options."
Rosenior confirmed he was part of the club's decision and added: "It's disappointing for Enzo to speak that way. I've got no bad words to say about him but a line was crossed in terms of our culture and what we want to build.
"Enzo, firstly, as a character, a person and a player, I have the utmost respect. He's frustrated because he wants us to be successful. The door is not closed on Enzo. It's a sanction. You have to protect the culture, and in terms of that, a line was crossed."
Fernandez joined Chelsea for a then-British record transfer fee of $205 million (£107 million) in 2023 and was appointed vice-captain the following year.
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