With just hours to go before the summer transfer window closed on September 1st, Manchester City's record-equalling £125M offer was accepted, and Fernandez made the move to the Etihad Stadium.
Chelsea were then thwarted in an attempt to sign AS Monaco playmaker Lamine Camara as a replacement and Alonso's midfield plans will now be tweaked.
The Spanish coach has revamped his squad in recent weeks and insisted there's no point discussing Fernandez following his departure.
"We take all of these decisions together. We work together on big ones and small ones. We knew ultimately the goal is to have the best for the team. We want to build a good spirit, a good team.
"In football many things happen. With Enzo we had conversations and always with respect. What he's done for the club has been great, but now it's time to move forward. We have players with quality in every position and now we are ready to go."
Chelsea head to Arsenal on Sunday in Alonso's biggest test since taking charge as he faces the defending champions and his old friend Mikel Arteta.