ABERDEEN conceded a late equaliser in Skopje after an alarming second-half display and in the end could easily have lost to Shkendija.
Scorers: Shkendija - Kirovski (85), Aberdeen - McGinn (79)
The Dons looked like they would take a first-leg Europa League lead back to Pittodrie for next week’s second leg after Niall McGinn opened the scoring with 11 minutes left.
But the goal was against the run of play after the Dons had faded badly after being dominant in the first half.
And they paid the price when they conceded a late equaliser, which was the least Shkendija deserved in Macedonia’s national Phillip II Arena stadium with just a few thousand fans in the vast ground, including around 200 Dons supporters.
Shkendija were ordered to move the first leg from their home city of Tetevo under UEFA regulations and the late kick-off also reduced the heat and humidity in the country’s capital.
The Dons – who were ordered to wear a combination of their away and home kits by the UEFA delegate due to a colour clash – started with on-loan Liverpool keeper Danny Ward and tucked new signing Graeme Shinnie into a holding midfield role.
The Scots soon settled down and Jonny Hayes tested the home keeper with a set-piece straight off the training ground when he dropped deep in the box to meet a Niall McGinn free kick. McGinn came close to giving the visitors a 21st-minute lead when he cut inside from the left before unleashing a low shot into the side netting.
Shinnie was having a fine competitive debut and a stirring run from the centre of the park through to the penalty box saw him tee up Hayes, but his former Caley Thistle team mate curled his effort over the bar.
Ward was tested for the first time on the half-hour mark after hesitant defending from Andrew Considine saw the ball fall for Victor Juffo, but his volley was straight at the new Dons keeper.
The home side were becoming increasingly dangerous as the half progressed and it took a brave block from Ash Taylor to deflect a fiercely-struck drive from Besir Demiri wide for a corner.
Shkendija continued to creep into the game, aided by some rusty defending from the Dons, and half-time sub striker Besert Ibraimi could have made a near instant impact if he hadn’t slipped when put through on goal by colleague Stenio Junior.
That at least jolted Aberdeen into action and Taylor missed a great chance with a free header from a Hayes corner when he nodded wide in plenty of space.
The excitable home fans were hugely encouraged, though, as Shkendija markedly upped the pace and as a consequence were seeing a lot more of the ball.
But the Macedonians came closest to the opening goal in the 61st minute when Ibraimi drifted free from a corner and glanced his header into the side netting, which sparked an inquest in the Aberdeen defence.
McInnes had seen enough and made a double switch with Willo Flood and the utterly-starved-of-service Rooney replaced by Peter Pawlett and David Goodwillie. Mark Reynolds then had to be replaced by new boy Paul Quinn after the defender suffered a clash of heads.
From being comfortable and confident earlier on, Aberdeen now looked in real danger of losing the game with too many Dons men making the wrong decision and looking increasingly rusty as the match wore on.
Quinn had to make a last-gasp tackle on Demiri as Shkendija again troubled Aberdeen on the counter-attack.
But just when it seemed there would be more misery for Scottish football in Europe, the Dons took the lead with 11 minutes left. Shay Logan scampered down the right and clawed back a fine cutback from McGinn to bundle into the net.
Yet they failed to hold on to the lead and the home side grabbed a deserved equaliser with five minutes left when sub Hristijan Kirovski nodded a looping header over Ward.
Shkendija: Jovanovski, Dzemaili (Kirovski 83), Cuculi, Alimi, Demiri, Polozani, Todorovski, Junior, Juffo (Bejtulai 80), Vrucina (Besar 46), Hasani.
Subs Not Used: Azizi, Demir Imeri, Bojku, Totre.
Aberdeen: Ward, Logan, Taylor, Reynolds (Quinn 9), Considine, Flood (Pawlett 64),Jack, Shinnie, Hayes, McGinn, Rooney (Goodwillie 64).
Subs Not Used: Brown, McLean, Smith, Robson.