Ryan Christie put Scotland ahead in the 31st minute, but Slovenia responded after the interval through Aljoša Matko before Danijel Sturm completed the comeback to hand the visitors all three points.
Christie puts Scotland ahead
Scotland struggled to establish control during the opening stages, with Slovenia creating the better early opportunities.
The visitors came close to breaking the deadlock when Adam Gnezda Čerin failed to make sufficient contact with a promising chance inside the penalty area.
Scotland eventually found their breakthrough in the 31st minute.
A short free-kick created an opening on the left, with Ben Gannon-Doak's deflected cross eventually falling to Ryan Christie, who finished from close range to give the hosts a 1-0 advantage.
Slovenia respond after half-time
Scotland carried their lead into the interval, but Slovenia returned with renewed purpose.
The equaliser arrived in the 56th minute after Scotland lost possession from a throw-in. Danijel Sturm drove through the middle before finding Aljoša Matko, who brushed aside Luis Binks and fired past Angus Gunn.
The goal shifted the momentum firmly towards Slovenia, who began to expose gaps in the Scottish defence.
Sturm completes Slovenia's comeback
Scotland were unable to regain control as Slovenia continued to threaten.
The visitors completed their comeback in the 74th minute, with Matko turning provider after bursting down the right flank.
His cross found Danijel Sturm, who arrived unmarked and finished past Gunn to put Slovenia 2-1 ahead.
The goal sparked frustration among the home supporters, with Scotland unable to find a response during the closing stages.
Scotland 1-2 Slovenia
• Scotland: Ryan Christie 31'
• Slovenia: Aljoša Matko 56', Danijel Sturm 74'
Scotland's poor second half proves costly
The defeat was particularly disappointing after Scotland had entered the match with confidence following their 2-0 victory over North Macedonia in Skopje three days earlier.
That victory had given Pocognoli his first win as Scotland manager, while captain Andy Robertson marked his 100th international appearance.
Scotland's latest defeat, however, exposed defensive weaknesses and leaves the new manager with plenty to address before the next international window.
Slovenia move second in Group B1
The result significantly improves Slovenia's position in UEFA Nations League Group B1.
Slovenia move onto seven points, while Scotland remain on four points. Switzerland lead the group with 12 points after their 3-0 victory over North Macedonia.
Scotland's remaining group fixtures will come in November, when they face North Macedonia at home before travelling to Switzerland.
Pocognoli faces questions after difficult start
Pocognoli's first international window has produced mixed results.
Scotland drew 0-0 with Slovenia earlier in the window, defeated North Macedonia 2-0 and have now lost 2-1 at home to the same Slovenian side.
The Belgian manager now has the November fixtures to demonstrate that his vision can translate into consistent results as Scotland attempt to climb Group B1.
For Slovenia, meanwhile, the comeback represents a significant away victory and keeps their hopes of finishing at the top of the group firmly alive.