Scotland failed to take their chances in the first-half
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Scotland Under-21 coach Archie Knox suffered a disappointing start to his new role after defeat in Slovenia in the European Championship qualifier.
The young Scots must now defeat France by a substantial margin at Pittodrie on 1 September to have any chance of qualifying for the Euro play-offs.
Steven Naismith, Calum Elliot and Zander Diamond all went close for Scotland in the first-half.
But Miran Burgic pounced on a rebound to score the only goal on 58 minutes.
The home nation went closest to open the scoring in the early stages when a Valter Birsa shot flew wide in the 10th minute.
Borut Semler tested Scotland goalkeeper David Marshall moments later but the Celtic player was equal to the shot.
Kilmarnock's Naismith drilled in a 10-yard strike moments later but Slovenian keeper Samir Handanovic was able to clear.
Hearts striker Elliot almost pounced on the rebound but defender Dejan Kelhar was faster to the ball.
Five minutes before the interval, Dalibor Stevanovic saw an effort fly wide before Aberdeen defender Diamond went close in the 43rd minute.
But an improved Slovenian display in the second period saw them clinch the win.
Semler found Stevanovic 12 yards from goal with his clever pass and the Real Sociedad player's effort was saved by Marshall.
However, the ball fell only to Burgic who slotted home comfortably.
Slovenia had another good opening in the 75th minute, when Birsa found Burgic, but Marshall saved his effort.
Scotland almost equalised in the 86th minute from their only opportunity in the second half.
Celtic striker Craig Beattie tried to beat Handanovic from the right with a powerful shot that flew just past the post.
Stevanovic could have added a second for the home side in the final minute, but his strike was wide of the target.
Slovenia U21: Handanovic, Brecko, Bojan Jokic, Rok Bozic, Kelhar, Pahor (Travner 65), Semler, Vrsic (Pecnik 79), Burgic, Dalibor Stevanovic, Birsa (Kronaveter 90). Subs Not Used: Nenezic, Hadzic, Cvijanovic, Tomazic-Seruga.
Booked: Bojan Jokic, Pahor, Dalibor Stevanovic, Brecko. Goal: Burgic 57.
Scotland U21: Marshall, Whittaker, Wilson, Thomson, Diamond, Broadfoot, Brown, Naismith, Elliot (Foster 75), Adam (Beattie 66), Wallace (Rocco Quinn 66). Subs Not Used: Samson, Paul Quinn, McEveley, McCormack.
Booked: Thomson, Diamond.
Att: 2,250
Ref: M Mikolajewski (Poland).