Scott Gemmill’s men were hoping to breath fresh impetus into their Under-21 Euro 2021 bid following back-to-back blanks against Lithuania and the Czech Republic.
But they again failed to take their chances and paid the price as Dimitris Nikolaou tucked home a stoppage-time penalty after Daniel Harvie had handled in the box.
The defeat will sting all the more given the visitors had played the final 27 minutes a man light after Bayer Leverkusen youngster Panagiotis Retsos was dismissed.
Gemmill’s team started the night leading Group D but dropped to third, two points behind the Greeks who took over at the top.
Nikolaou held his nerve at the death but Scotland should have put the game to bed long before that.
A sublime Billy Gilmour flick set Jamie Brandon surging forward four minutes in before the Hearts youngster slipped a reverse pass to Allan Campbell, but the skipper wasted the opening as he pushed wide.
Jordan Holsgrove shaped to flight the ball into the box from a free-kick out wide, but teed up Gilmour, pictured, for a strike which zipped just over Marios Siampanis’ bar.
Campbell did find the net eight minutes before the break from Stephen Kelly’s cross but his effort was ruled offside, while Holsgrove to fizzed another strike just off target before the interval.
Greece had barely threatened in the first half and the odds looked against them in the 63rd minute as Retsos was sent off. Already on a booking after a late tackle on Gilmour, the Greek captain clattered into the Chelsea midfielder again and was shown a second yellow.
But Scotland failed to make the most of their man advantage, and the sucker punch arrived as Harvie inexplicably threw an arm out at the ball with the 90 minutes almost up. Nikolaou did not blink as he rolled the ball past Ross Doohan to leave the Scots dejected.