Amorim, 41, was sacked in January after a disastrous 14 months in charge and replaced by former midfielder Michael Carrick.
Carrick has been a revelation, turning things around at Old Trafford and securing champions League football with a third place finish.
Asked about Carrick's impact after collecting his Footballer of the Year prize at the Football Writers' Awards ceremony, Fernandes told Sky Sports News: "When the change was made, we were not far from what we wanted (to achieve) this season. That was the top four.
"At the same time, it was in need of change by the club for different reasons – I won't be naming them now.
"Me and the boss (Michael Carrick) spoke before, and we said we can play better, we want to play better.
"We didn't achieve the level we want to have, but since he came, the results show we were one of the best teams in the Premier League."