Fernandes won the ball in midfield, played a one-two with Manchester United team-mate Cristiano Ronaldo and fired home from the edge of the box to open the scoring in Porto.
He then volleyed in Diogo Jota’s cross for the second having helped start the move himself outside his own box.
The Macedonians, who stunned Italy in the semis, offered little throughout.
They never looked like reaching a first World Cup and failed to test Portugal goalkeeper Diogo Costa once.
Portugal qualify for their sixth World Cup in a row with Ronaldo, 37, going to the tournament for a fifth and potentially final time.
Fernando Santos has led his country to Euro 2016 and the 2019 Nations League and is now targeting their first ever World Cup crown.
“I have already won two competitions and I hope I can win the third one in Qatar,” coach Santos said.
“There was a spirit of mutual help and great support from the public. It was a deserved and fair win and qualification. I don’t remember any great goalscoring situations for their team.”
Portugal sealed their World Cup spot four and a half months after they had hoped to. They were seconds away from winning their group before Aleksandar Mitrovic’s 90th-minute goal sent Serbia through instead.
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