The result, coupled with Spain's 3-0 win over Albania, ensured that Italy will finish second in Group G although they are not yet certain of making the playoff round.
Italy, under fire since their comprehensive 3-0 defeat by Spain last month, seemed to have done the hard part when Giorgio Chiellini scored to break down the visitors' defence five minutes before halftime.
But the goal failed to inspire the four-times world champions and they were stunned when Aleksandar Trajkovski, who plays for Palermo in the Italian league's second tier, equalised in the 77th minute.
Italy have 20 points in Group G and their hopes of reaching Russia now rest on finishing as one of the best eight runners-up who progress to the playoff round from the nine European groups. The group winners all qualify directly.
However, the prospect of deciding their fate in a two-leg tie has made the Italian media and fans jittery and recent performances have added to fears that the unthinkable may happen and Italy could fail to qualify for the first time since 1958.
Coach Giampiero Ventura blamed Italy's poor fitness levels for their dismal second half.
"That made a big difference and when that drops, the sharpness goes," he said.
“I think Italy should never be jeered, as the team represents all of us," he added. "I thought the first half was positive, the second was not, but when you run out of gas, that's what happens."
Italy visit Albania in their final game on Monday.
Lorenzo Insigne created a good early opening for Italy after a quick exchange of passes with Ciro Immobile but Stole Dimitrievski rushed out to save.
Insigne then provided a pass which allowed Davide Zappacosta to get behind the defence but he sliced his effort high and wide.
Italy went ahead when a session of head tennis ended with Insigne slipping a ball through the Macedonia defence to release Immobile on the left and he laid the ball off for central defender Chiellini to tap in from close range.
Chiellini came to the rescue at the other end less than a minute later, rushing across to clear the danger after defensive partner Leonardo Bonucci gave the ball away.
Italy failed to click after halftime and were given a first warning when Gianluigi Buffon had to smother a header from Ilija Nestorovski.
The equaliser came when Goran Pandev sent Trajkovski clear and he drove an angled shot wide of the veteran goalkeeper.
(Writing by Brian Homewood; Editing by Toby Davis)
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