Elmas slotted in after the four-times world champions had controlled the game but struggled to create chances against the disciplined North Macedonians, ranked 65th in the world.
It was Germany’s first home World Cup qualifying loss in 20 years in coach Joachim Loew’s last qualifying game in charge ahead of his departure following this summer’s European Championship.
Despite Germany’s 70 per cent possession in the first half and Leon Goretzka’s shot onto the crossbar, it was the visitors who scored when 37-year-old Goran Pandev was left unmarked in the box to tap home in first half stoppage time.
A 63rd-minute Ilkay Gundogan penalty drew the hosts level but despite late pressure and a golden chance for Timo Werner 10 minutes from time, Germany could not find a winner.
Instead, it was Elmas who scored to lift North Macedonia to six points, level with Germany in Group J and three behind leaders Armenia.
Meanwhile, England’s Harry Maguire smashed home a late winner as they laboured to a 2-1 win over Poland, with the defender bailing out team mate John Stones whose error nearly cost the hosts all three points.
Maguire swivelled and smashed home a knock-down from a corner in the 85th minute to maintain England’s perfect start to their Group I campaign.
England had dominated the majority of the match at Wembley, taking the lead after 19 minutes when Harry Kane fired home from the penalty spot. Things turned sour for Gareth Southgate’s side, however, when Stones allowed Jakub Moder to level in the second half.
Stones dawdled on the ball and Poland midfielder Moder robbed him of possession before firing home after a quick exchange of passes.
The win lifted England to nine points from three games, two ahead of Hungary in second with Poland on four points.
Antoine Griezmann struck again as France extended their Group D lead to four points with an unconvincing 1-0 away win against Bosnia.
Griezmann, who scored in last Wednesday’s opening game against Ukraine, put the world champions on seven points from three games.
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