The Argentina international was harshly shown a straight red card by referee Keith Stroud for a challenge on Philippe Coutinho in the 92nd minute of the fourth round clash at Anfield.
Swansea's misery was further compounded when Dejan Lovren headed home the winner shortly after to ensure Liverpool progressed with a 2-1 victory.
Speaking after the game, Swansea manager Garry Monk labelled the decision incorrect and, unsurprisingly, the Welsh club have now appealed against Stroud's decision.
"Swansea City can confirm that the club will be appealing the red card issued to defender Federico Fernandez against Liverpool last night," read a statement on the club's official website.
"The club officially informed the Football Association by [Wednesday's] deadline.
"The Argentinian defender, who faces a three-match ban, was shown a straight red card by referee Keith Stroud for a tackle on Philippe Coutinho during stoppage time in the 2-1 Capital One Cup defeat at Anfield.
"The FA will make a decision on the appeal ahead of Saturday's Premier League trip to Everton."
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