Hibs take a one goal lead to North Macedonia next week, but in truth it wasn’t a game that will live long in the memory.
David Gray went with the same starting line-up from the defeat by Motherwell at the weekend.
Shkendija made three changes from their 3-1 victory over Slovenian side Bravo in the previous qualifying round.
In goals, Ferat Ramani replaced Astrit Amzai, while outfield, versatile defender Bojan Dimoski and midfielder Sebastjan Spahiu were replaced in the starting line-up by Jovan Manev and Endrit Krasniqi.
In a lacklustre first-half, the only talking points were a superb tackle from Miguel Chaiwa to deny Fabrice Tamba’s shot from the edge of the box.
And in the last action, Martin Boyle went down inside the box under a challenge from Arbin Zejnulla but the referee waved play on.
There was a slight improvement in the second-half with hibs showing some more urgency, particularly after a double substitution when Ante Suto and Callum Wright replaced Boyle and Adam Mayor.
And it was sub Wright who made the opening goal in the 71st minute when he beat two defenders down the left wing and fired in a low cross which Owen Elding knocked into the net from close range.
The Hibs fans thought that would open the floodgates but the visitors equalised moments later following some poor defending which allowed substitute Marko Gjorgievski space to slot the ball into the bottom corner of the net.
It looked as though the game would end in a draw but Hibs won it at the death.
Jordan Obita sent a corner towards the back post and Warren O’Hora was on hand to knock the ball into the net from two yards.
After the final whistle Gray told BBC Scotland: “In terms of being at home and trying to have that home advantage, it’s a big moment to go in front.
“It’s hard to win games in European football, so to be winning after the first leg is very positive.
“It’ll be very different when we go over there, but I think we’ll be different. I can’t stand here tonight and say we deserved to be further in front. It will be a very different game with us being in front – they’ll have to come out a little bit.
“You need to enjoy that winning feeling. The players can be happy with the fact that we’ve won the game. We’ll play better. I thought we played better on Saturday even though we lost the game.
“The biggest thing is you take the positives and the confidence from that, but we’ll have to quickly put that to bed and look forward to Rangers on Sunday.”
Hibs: Sallinger, Passlack, Kerr, O’Hora, Obita, Mulligan, Chaiwa, Mayor, Elding, Boyle, Lowe.
Substitutes: Smith, Owens, Hanley, Newell, Klidje, Molotnikov, Suto, Wright, Megwa, J MacIntyre, Campbell, Abdulai.
Shkendija: Ramani, Trumci, Manev, Melliqi, Zejnullai, Rafael Freitas, D Islami, Tamba, Krasniqi, Kryeziu, Ndzengue.
Substitutes: Amzai, B Ibraimi, Murati, Ceka, Krstevski, Isa, Spahiu, Ramadani, Gjorgjiveski.
Attendance 15,132
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