From the set-piece Gordon brilliantly touched Macedonia captain Sedloski's strike onto the post, but Naumoski followed up to drill the ball low into the net.
Jermain Defoe, who has been linked with a move away from White Hart Lane but was captain on the day, slowly came into the game and only a Gordon fingertip save prevented his cheeky chip from doubling Spurs' lead.
The manager, who arrived from West Brom during the summer to succeed Gordon Strachan, also recently said that there was no guarantee that McManus would remain captain on his return from injury.
The former England Under-21 captain returned to the Boro side after a groin injury in order to strengthen the options for boss Gordon Strachan, in the Teessiders' third meeting with Billy Davies' East Midlanders this season.