Shane Burger's Scots - who defeated Papua New Guinea the previous day - completed their innings on 137 for eight.
But the Namibians hit back to reach 138 for five within 18 overs as Craig Williams celebrated a half-century before losing his wicket to Dylan Budge.
Coach Burger admitted his side were not at their best as he told Cricket Scotland: "It was a below-par performance in terms of the standards and expectations that we've set."
Scotland batted first and Richie Berrington led the way with a knock of 61 which took him over the 1,500-run landmark in T20 Internationals, but his fellow batsmen struggled to hit the heights.
Burger added: "Richie was excellent with the bat. He really anchored the innings and showed his class."
Namibia chased down their target strongly, with Williams (50) and Stephan Baard (39) their main run-scorers.
The Scots play their T20 World Cup first-round match against Bangladesh in Oman on Sunday, October 17.
Captain Kyle Coetzer said: "“It was not the result we were after, [but it was] nonetheless a good run out in the field and a good test to put our batting line up under pressure.
There's definitely a little bit of room for improvement, but we're on the right track.
"The guys are playing well and I fully expect them to bounce back when the World Cup period starts."