Dons winger Niall McGinn’s strike in Macedonia in the opening leg proved crucial after a goalless night at Pittodrie.
The hosts went closest when midfielder Peter Pawlett stuck the crossbar with a superb dipping shot from 25 yards out in the second half.
After a slow start, Shkendija’s Armend Alimi went close, with the away side looking dangerous on the break, with shot just the wrong side of the far post on six minutes from a cut-back from the byline.
Aberdeen settled into a rhythm after 20 minutes but, with the visitors desperately needing an away goal on the night, Juffo went close on the half-hour mark with a curling shot from the edge of the area.
The Dons had shouts for a penalty turned down just before half-time when McGinn’s shot was fumbled by Shkendija keeper Marko Jovanowski and the keeper appeared to take down Adam Rooney, but the referee showed little interest in their claims.
Agim Ibraimi went close late on as Shkendija pushed for a winner but the tie finished 1-1 on aggregate, sending the Dons through to their second qualifying tie next Thursday.