Dejan Lovren scored the winner after Fernandez's 92nd-minute dismissal to send the Reds through to the quarter-finals, but Monk promised to appeal the red card as he again cursed apparent refereeing injustices.
The Premier League's youngest manager described the award of a penalty against them in the 2-1 loss to Stoke City earlier this month as "disgusting", but was cleared by the FA this week. He will meet with referees chief Mike Riley on Friday to discuss bad decisions by officials.
While Roberto Martinez watches his former club struggle to match their early-season standards, he is slowly guiding Everton up the table thanks to contributions from both his most youthful and most senior players.
The result lifted the Toffees, who had a midweek off courtesy of their third-round defeat to Swansea, into the top half and to within two points of the Welsh side ahead of their meeting at Goodison Park.
Having been rested for the trips to Lille and Burnley, Barkley could be restored to the starting lineup, although Eto'o's recent brace and Steven Naismith's 2014 form mean that there is great competition for places.
Romelu Lukaku is expected to shake off a knock to continue as the spearhead of the attack, but another injury blow to Darron Gibson rules him out along with Kevin Mirallas, John Stones, Arouna Kone and Bryan Oviedo.
Should Fernandez's suspension be upheld, Kyle Bartley will deputise at centre-half, with alternative Jordi Amat sidelined. Monk is also sweating on Gylfi Sigurdsson's participation after the midfielder, who is the leading provider of goals in the division, missed the midweek defeat with a groin strain.
Everton have scored at least twice in their last 10 Premier League home games, and have never lost a league match to the Swans.
Possible starting lineups
Everton: Howard; Coleman, Jagielka, Alcaraz, Baines; Barry, McCarthy; Naismith, Barkley, Eto'o; Lukaku
Swansea: Fabianski; Rangel, Williams, Fernandez, Taylor; Shelvey, Ki; Dyer, Sigurdsson, Routledge; Bony
Sports Mole says: 2-1