The City midfielder started for Fernando Santos’ team alongside Etihad colleagues Ruben Dias and Joao Cancelo.
And in an impressive overall performance by the guests, Bernardo scored the opening goal in the 26th minute.
Fernandes was once again the supplier as his cross was supported by Diego Jota so Andre Silva could bring the finish.
And a good night job for Portugal was sealed with 12 minutes left when Jota scored a third goal and Bernardo was then replaced by Otavio.
Second-placed Serbia, who has 10 points, will play away against the Republic of Ireland tonight.