Fernández's absence from Thursday's win over Luton Town came as a surprise given Alonso had said the day before that he intended to use the Argentinian.
The head coach explained his reasoning without directly addressing the speculation linking Fernández with a £120m move to Manchester City.
"We need the players that are in the best situation to play. We need to take everything into consideration — players that are in a good moment, players that are not feeling that energy to play. For me, it is very important they feel this desire to play and to have good preparation," Alonso said.
Alonso revealed he had spoken with Fernández directly before making the decision.
"We talked and we decided it was better not to be part of the squad. He is a top player," he said.
Chelsea sources maintained on Thursday night that no formal approach had been received from City despite the growing speculation, even as Fernández's omission fuelled talk that club-to-club talks were already under way.
Asked whether Chelsea would need to find a replacement should Fernández leave, Alonso declined to be drawn into hypotheticals with days still remaining before the deadline.
"Sorry, but I'm not the one who talks too early. We will see what happens. We want to be ready always," he said. "We are quite close to the plan we had. We will see where we finish, if it's fully executed or there are things still to be done or things we couldn't do.
"But overall the balance of what we have is going to be good. We have to see how the last few days develop. The team is coming together."