- Enis Bardhi (41')
- Jani Atanasov (59' OG)
With qualification long since secured and just a draw needed to seal a top seeding for next year's finals, England trailed to Enis Bardhi's 41st-minute follow-up after his penalty was saved.
Gareth Southgate's group winners hogged possession but lacked fluency and invention against dogged hosts and needed an own goal by Jani Atanasov to get them level on the hour.
England ended the calendar year unbeaten, if in a rather underwhelming way, topping their group with 20 points from eight games with North Macedonia fourth on eight points.
"The really big results were in March, winning in Italy and the result against Ukraine (2-0 home win)," Southgate, whose side thrashed North Macedonia 7-0 at Old Trafford, said.
"It meant coming here tonight was a different test, given we've qualified and everything was achieved."
England would have hoped to have finished with a flourish but they got bogged down with slow passing and the biggest positive was that they will be in the pot of top seeds for the Euro 2024 draw.
Southgate made six changes to the side that started Friday's game versus Malta with Ollie Watkins getting a chance to impress in place of the rested Harry Kane and full back Kyle Walker wearing the captain's arm-band for the first time.
Watkins had only 11 touches, however, as England lacked creativity and was replaced by Kane in the second half.
Manchester City youngster Lewis could be happier with his performance and was extremely unlucky to concede a penalty.
In heading away a bouncing ball he inadvertently caught Bojan Miovski in the face with his hand, prompting a VAR check which eventually saw Slovakian referee Filip Glova award a spot kick after checking the pitch-side monitor.
Jordan Pickford saved Bardhi's effort but the rebound fell invitingly to Bardhi who made no mistake at the second attempt.
It was tough on Lewis although England were fortunate earlier when Harry Maguire bundled over Elif Elmas in the box after his initial sloppy pass had put his side in trouble.
Grealish then thought he had levelled from Bukayo Saka's cross two minutes after the restart but he was ruled offside after a lengthy VAR check.
It took the introduction of captain Kane to finally get England back on level terms.
Seconds after replacing Watkins he attacked Phil Foden's cross and the ball went in off Atanasov.
North Macedonia held on for the draw though as England failed to beat a side ranked as low as 66th in the FIFA rankings for the first time since 2016.
It was also only the third time in 26 European Championship qualifiers that England failed to win, although Southgate sounded a positive note.
"The next exciting bit is the draw at the beginning of December and we will see what the path looks like," he said.
- Filip Glova