New Democrat Amanda Lathlin won the northern constituency with 57 per cent of the vote — down sharply from the 73 per cent the NDP captured in the last provincial election.
The Progressive Conservative and Liberal candidates both saw their takes rise.
NDP support also dropped in two Tory-won byelections last year — in Morris and Arthur-Virden — following the sales tax increase.
Political science professor Paul Thomas, at the University of Manitoba, says the results are not a good sign for the New Democrats, who have already seen support in opinion polls plummet to near record-low numbers.
He says given the fact the NDP just had a leadership race and signed up new members, their numbers in The Pas ought to have been higher.
"You would have thought they had a better ground game in terms of identifying potential supporters and getting them out," he said Wednesday.
The result Tuesday in The Pas suggests traditional NDP support splintered. The Liberals gained 10 percentage points, the Tories gained seven and a record number of people stayed home.
Voter turnout was 22 per cent, the lowest ever recorded by Elections Manitoba and down from 30 per cent in both the last election and a 2009 byelection.
Thomas said no one can write off the NDP's chances of winning a fifth consecutive mandate in the election slated for next April, but time is short.
"It's an uphill battle, to say the least. It's more like a tremendously steep climb out of the depths of political downfall."
Premier Greg Selinger was in Churchill and unavailable for comment.
Progressive Conservative Leader Brian Pallister said the drop in NDP support bodes well for his party's chances in many Winnipeg seats, where the Tories finished a close second in 2011.
"If that happens across the province, that'll be a fine thing."