Matt Machan was bowled out for 48 by Bernard Scholtz, who took three wickets for Namibia, while Calum McLeod was in good touch to score 71 runs off 102 balls as Scotland set their opponents a target of 276 to win.
Namibia took a while to get going in their response and had only scored 158 runs when Jaen Kotze (43) lost the seventh wicket to Rob Taylor.
The Leicestershire bowler took four wickets in total and Namibia found themselves restricted to just 212 for nine by the end of the 50th over.
Gerry Snyman did, however, find the boundary eight times and claimed the match's best batting score of 73.
Scotland, who also beat Papua New Guinea while warming up, face Hong Kong in World Cup qualifying Group A in Queenstown on Monday.