David Bright's charges scored their first goal in 362minutes of football, when they found the net in the third minute, but the hosts rallied back to secure the win, which guaranteed them progress to a first ever Africa Cup of Nations finals appearance.
While Mauritania celebrated wildly at the end of the match, there were long faces on the Botswana bench, with questions over Bright's future refusing to go.
Last month, ahead of the team's clash against Burkina Faso in Francistown, Bright insisted that he would not resign, instead, blaming his employer, the Botswana Football Association (BFA) for lack of support.
the campaign without a win, Bright's future has been dragged back into focus.
The Zebras squandered a perfect opportunity to replicate their 2012 heroics when they qualified for their first ever AFCON finals. For the 2019 qualifiers, the job had been made easier after CAF increased slots from 16 to 24, meaning the top two teams qualify.
But even if number three was in contention, the Zebras would still be a long way off, as they have just one point, six behind third placed, Burkina Faso.
This will go down as one of the worst Zebras records in recent history, with soul searching expected to begin as soon as the team lands.