Three days on from an unconvincing 2-0 win over Malta, the Three Lions controversially fell behind to an Enis Bardhi penalty rebound before restoring parity through Jani Atanasov's own goal, thereby ensuring that they would conclude Group C unbeaten.
With Kieran Trippier departing the camp for personal reasons, Southgate brought in Manchester City left-back Rico Lewis for his senior debut, and the 18-year-old - who turns 19 on Tuesday - let fly with the first attempt of the game in the fourth minute, although his effort was high and not very handsome.
The Three Lions had settled into a dominant period of possession, though, and Declan Rice was the next to try his luck with 14 minutes gone, only to see his powerful long-range drive cannon off the post before North Macedonia managed to clear.
Blagoja Milevski's side soon resorted to chopping down their opponents in an attempt to quell their momentum, but the home fans were the ones up in arms in the 24th minute, as Harry Maguire sloppily gave the ball away in a dangerous area before clattering into Eljif Elmas.
North Macedonia's appeals for a penalty ultimately fell on deaf ears as Maguire - who appeared to fall into Elmas - counted his lucky stars, but Lewis would not be so fortunate in the 39th minute, as in the process of heading away a cross, he caught Bojan Miovski in the face with his hand.
Miovski certainly made a meal of the contact, but Slovakian referee Filip Glova nevertheless awarded a spot kick after checking the monitor, and while Jordan Pickford kept out Bardhi's poor spot kick, the hosts' captain made no mistake on the rebound.
The luckless Lewis and Trent Alexander-Arnold were both denied by Stole Dimitrievski as England sought to get back on level terms in added time, and the visitors had two penalty appeals of their own turned down just before the half-time whistle blew, as Marc Guehi was bundled over before Maguire took a knee to the head.
England had largely failed to make inroads against the North Macedonians' low block, but the visitors had the ball in the back of the net just two minutes into the second half, as Bukayo Saka escaped the attention of two Lynxes defenders before crossing for Jack Grealish to finish at the back post.
However, replays showed that Grealish was in an offside position - which inexplicably took the VAR room a few minutes to ratify - but Southgate's side were finally rewarded for their endeavours in the 59th minute.
Another inswinging cross did the damage, as Phil Foden tried to pick out the head of the newly-introduced Harry Kane, who challenged for the ball with Atanasov and saw the North Macedonia midfielder deflect the ball into his own net.
Southgate's men huffed and puffed for a winner as the second half progressed, but slow build-ups, poor final balls and a whistle-happy referee all dented their hopes of another three-point haul, and they survived a scare when Nikola Serafimov's looping header in the 88th minute landed on the roof of the net.
Six minutes of added time was not enough for either side to snatch a winner, but England - who finish with 20 points to their name - will nevertheless enter the group-stage draw on December 2 as one of the top seeds alongside France, Portugal, Belgium, Spain and host nation Germany.
Meanwhile, North Macedonia had already been condemned to missing out on a second straight Euros appearance after making their major tournament debut two years ago, as Italy nabbed second spot in Group C owing to their 1-1 draw with Ukraine, who will have a second shot at qualification via the playoffs.