Fernandes fires Portugal to victory at Slovakia on birthday
Roberto Martinez's side have not conceded a goal in Group J, scoring 15, and are five points clear of their opponents who are second after being beaten for the first time.
"We knew it would be complicated but we managed to unlock the game," Fernandes told Portuguese broadcaster RTP.
"We needed to have a little more of the ball, to be more patient."
With veteran defender Pepe, 40, injured, the Portugal coach selected 19-year-old Benfica defender Antonio Silva alongside Ruben Dias at the centre of defence.
Cristiano Ronaldo, making his 201st Portugal appearance at the age of 38, scored against Slovakia back in 2005 in a World Cup qualifier, one of a record 850 career goals, but could not add to the tally on this occasion.
The former Manchester United and Real Madrid forward made his Portugal debut back in 2003 and has more international goals, with 123, and appearances than any other player.
Ronaldo had his arms up in anguish after Fernandes shot instead of passing after a Slovakia defensive mix-up, with Martin Dubravka saving the midfielder's low effort.
It was one of few chances in a cagey first half, with Slovakia keeping things tight, although the hosts could have gone ahead when Lukas Haraslin brushed the outside of the near post with a fierce drive.
Moments later Fernandes sent Portugal ahead, drilling home from a tight angle into the far corner, his third goal of the qualifying campaign sending the visitors in ahead at the break.
Ronaldo miscued after an hour when he might have doubled Portugal's lead and then slid in on Dubravka while trying to turn home the loose ball to earn a yellow card.
The forward will be suspended for the Euro 2016 winners' next game, against Luxembourg on Monday.
Ronaldo missed another good chance when well placed with 15 minutes remaining when Dubravka saved his near post effort comfortably, but Portugal held on for the win.
"Our focus is on the next game," added Fernandes, when asked if the team were sure they would qualify.
"We know what it takes to be at the Euros, but what we want is to win every game."