The Manchester United midfielder scored a goal in each half as Portugal booked their place to Qatar later this year.
The result sees Portugal qualify for the World Cup for a sixth consecutive time. It is likely to be Cristiano Ronaldo‘s last for his country although he dismissed reports of retirement before the playoff.
Macedonia were unable to replicate their shock win over European champions Italy but gave a good account of themselves throughout the 90 minutes.
Portugal took the lead after 22 minutes when Fernandes intercepted a poor pass in midfield and exchanged passes with Ronaldo before producing a fine finish into the corner.
Portugal controlled the match from that moment and doubled their lead in the second half after 65 minutes when Fernandes got on the end of a fine counter attack to convert from close range.