Aberdeen survived a testing second half in Skopje as Hristijan Kirovski's equaliser for Shkendija cancelled out Niall McGinn's opener.
The Dons had been in control of the first leg of the Europa League first qualifying round tie during the opening 45 minutes against the Macedonians.
Just as Shkendija appeared dangerous, McGinn's scuffed shot from Shay Logan's cross looked to have won the game.
But sub Kirovski's looping header levelled the game five minutes later.
Aberdeen had pitched goalkeeper Danny Ward, on loan from Liverpool, straight into European action, while fellow new signing Graeme Shinnie found a berth on the left side of midfield.
The Dons threatened early on when Jonny Hayes connected with a free kick inside the penalty box, but he could not get enough power into the shot and goalkeeper Marko Jovanovski held the effort.
Aberdeen were the dominant side, enjoying the majority of possession and not looking in any discomfort, while Ward dealt briskly with Victor Juffo's snap volley on the half hour.
Besir Demiri's effort was blocked for a corner by Ash Taylor as the Macedonian's threatened again.
The home side started much more brightly in the second half and the introduction of substitute Besart Ibraimi, the Macedonia striker signed during the summer, lifted their threat level several notches.
Ibraimi's first involvement was poor as he slipped as he prepared to shoot after being set up by Stenio Junior, but he then cracked a powerful long-range free-kick that Ward tamed without fuss.
Aberdeen broke upfield and McGinn powered a fierce effort goalwards, but a flying leap and clutch from Jovanovski saved a certain goal.
Ibriaimi again threatened with a glancing header that narrowly missed the target.
Worryingly for Aberdeen, defender Mark Reynolds suffered an arm injury and had to leave the field to be replaced with summer signing Paul Quinn.
Logan made a saving tackle to clear the danger as the Dons defence was pierced with 15 minutes to go.
It was McGinn, though, who broke the deadlock, clipping home from 10 yards to score after a neat Logan cross from the right found him unmarked.
Aberdeen could not keep Shkendija at bay, however, and, with five minutes left of normal time, substitute Kirovski's powerful header left Ward helpless.
McGinn almost restored the Dons lead in the dying embers of the game, but Jovanovski blocked the shot with his chest to ensure the sides go into next Thursdays' second leg at Pittodrie level as they battle to face Rijeka of Croatia in the next round.
- 3AbdulaSubstituted forKirovskiat 84'minutes
- 11DemiriBooked at 54mins
- 18da Fonseca Salazar Junior
- 24HasaniBooked at 36mins
- 10VrucinaBooked at 23minsSubstituted forIbraimiat 46'minutes
- 20JuffoSubstituted forBejtulaiat 80'minutes
- 6ReynoldsSubstituted forQuinnat 69'minutes
- 8FloodSubstituted forPawlettat 65'minutes
- 9RooneySubstituted forGoodwillieat 65'minutes
- Tolga Özkalfa