England had sealed qualification for next year's finals in Germany with two games to spare and Monday's draw saw them go through Group C unbeaten.
Gareth Southgate's side fell behind in Skopje after debutant Rico Lewis was penalised for a foul inside the box and Enis Bardhi scored on the follow-up after his penalty was saved.
They got back on level terms in the second half via an own goal from Jani Atanasov.
"Difficult game, we knew it would be and it was tough against a decent side playing on a pitch that is difficult to play our style of football on," Kane, who came on in the second half, told Channel 4.
"If anyone was going to get a second (goal) it was us. We can be really proud of how the qualifying campaign has gone."
Full back Kyle Walker, who wore the captain's armband for the first time, said England should have won the match.
"It's been a short week, two games when we've already qualified," he added. "It's no excuses, we know we should be taking three points from here but it's something to work on for the future."
