The Scots had racked up 279 for nine and had their opponents 59 for two after 12.1 overs of their reply when rain prevented any further play on Sunday carrying the match over into Monday's reserve day.
And when play resumed, Safyaan Sharif claimed four for 55 ro help restrict Namibia to 258 for nine.
Scotland now face two further games against Papua New Guinea and Kenya and need to finish in the top two in the six-team group to qualify for the World Cup in Australia and New Zealand in 2015.
Scotland won the toss and decided to bat but were handed a blow when Calum MacLeod, who had scored 175 against Canada in the final group game, departed for just 10.
Fellow opener Matty Cross then fell for 27 but Matt Machan and skipper Preston Mommsen put on 82 for the third wicket to guide Scotland to 154 for two.
Machan eventually fell for 78 after bringing up his half-century off just 33 balls and Mommsen soon followed for 46.
But the Scots were getting good contributions from their middle-order and Freddie Coleman scored 32 before being dismissed by Bernard Scholtz who was the pick of the Namibian bowlers with three for 55.
Rob Taylor (four) and Michael Leask (eight) both fell cheaply but Richie Berrington was holding the innings together and he brought up his half century off 46 balls before falling for 51.
Majid Haq (three) was the other wicket to fall as the Scots managed to set what looked to be a competitive total.
Louis van der Westhuizen was the first to fall in reply as he went for just nine, caught by Machan off Taylor.
Sarel Burger was then clean bowled by Taylor to leave Namibia 39 for two before Stephan Baard (28 not out) and Craig Williams (eight not out) held the fort until the rain came.
When play resumed on Monday, Baard was first to fall for 36 as he was run out but Williams and Nicolaas Scholtz put on 80 for the fourth wicket before the latter was bowled by Sharif for 38.
Williams had brought up his half century off 76 balls but he was next to go for 57 as Sharif claimed another victim to leave Namibia 166 for five with 13 overs remaining.
Christi Viljoen followed for just two and after that Namibia were never able to get near the required rate.