Jota made it 5-0, Ricardo Horta got a sixth and Jota added a seventh.
Fernandes, who also made three goals, scored the eighth and former Chelsea player Joao Felix added a late ninth.
Manchester United midfielder Fernandes created the first goal with a cross from the right wing with the outside of his boot and also was involved in the build-up to Portugal's fourth and fifth goals.
It means Portugal have won all six of their Euro 2024 Group J qualifying matches since Roberto Martinez became head coach in January when he replaced Fernando Santos, who resigned after Portugal's quarter-final defeat by Morocco at the World Cup in Qatar.
Leaders Portugal have scored 24 goals in their six matches and conceded none.
They will qualify for next summer's Euro 2024 in Germany with three games to spare if they win at home against second-placed Slovakia on 13 October and third-placed Luxembourg fail to win away at Iceland.
Earlier on Monday, Luxembourg's under-21 side lost 3-0 to England in a European Under-21 2025 qualifier.