Sean Lineen's side had lost their opener against Georgia on Friday and the youthful Scottish outfit once again let slip an early lead as they succumbed to a full-strength Namibian national team who are en route to next year's Rugby World Cup in New Zealand.
But they made a strong start here as they moved into a 10-0 lead courtesy of a try from centre Bryan Rennie plus a penalty and conversion from fly-half David Blair. The Namibians hit back as scrum-half Eugene Jantjes went over for an unconverted try and Chrysander Botha kicked a penalty, although Blair's second penalty gave Scotland A a five-point lead.
But further tries from hooker Shaun Esterhuizen and replacement Tinus du Plessis helped put Namibia in control at 23-13.
In the final ten minutes, Scotland continued to attack. With some positive phases of play, they eventually had the Namibian forwards under heavy pressure in the corner. But as the backs were released, David Blair's replacement, younger brother Alex, knocked the ball as he was tackled on his way between the posts.
In the dying moments, replacement scrum-half Greig Laidlaw converted his own try to set up a tense finish, but Namibia held on and the game ended when they threw the ball out of play.
Laidlaw said: "Everyone is absolutely gutted. We never put right the wrongs from the first game and they came back to haunt us once again.
"We have to look after the ball and go through the phases and we just aren't doing that.
"We've now got to pick ourselves up, dust ourselves down, and we must beat Argentina. We've got to put some pride back in the jersey and we've got to put in a performance for the sake of the jersey because the two games we've played are unacceptable."
Head coach Sean Lineen added: "In the beginning, we played how we had trained. We played well and in the first half we were ahead. "But then just a combination of lack of skill, lack of composure and being able to handle the conditions – we just couldn't do it. The other team got its wind up and away they went."
The defeat leaves Scotland A fifth out of the sixth teams in the tournament. They will play Argentina Jaguars in their final game on Sunday.
Scotland A: Jack Cuthbert (Bath); John Houston (Edinburgh), Ben Cairns (Edinburgh), Bryan Rennie (Exeter), Mark Robertson (Edinburgh); David Blair (Edinburgh), Mark McMillan (Glasgow); Bruce Douglas (Montpellier), Andrew Kelly (Edinburgh), David Young (Edinburgh), Fraser McKenzie (Edinburgh), James Eddie (Glasgow), Ally Hogg (Edinburgh, captain), Chris Fusaro (Heriot's), Roddy Grant (Edinburgh). Substitutes: Scott Newlands (Edinburgh) for Fusaro 35mins, Fergus Thomson (Glasgow) for Kelly 50mins, Lewis Niven (Edinburgh Accies) for Young 48mins for Niven 53mins for Young 63mins, Greig Laidlaw (Edinburgh) for McMillan 50mins, Peter Horne (Glasgow) for Cuthbert 66mins, Ed Kalman (Glasgow) for Douglas 67mins, Alex Blair (Edinburgh) for David Blair 68mins.