Economists had expected a deficit of $100 million for September, according to Thomson Reuters.
The federal agency also cut the size of the trade deficit for August to $463 million compared with its initial estimate of $610 million.
CIBC economist Nick Exarhos said after last month's surprise deficit, the country's trade balance was back on a healthier footing in September.
The stronger than expected trade data followed a report last week that suggested the economy unexpectedly declined 0.1 per cent in August compared with July.
"A more upbeat trade report for September gives us hope that some of the temporary factors dampening prior months' readings won't weigh on the GDP figure for the quarter’s last month," Exarhos said.
"However, even if we were to get a strong GDP report to close out the third quarter, we aren't likely to match the Bank of Canada's 2.3 per cent forecast. That's a reason why the Bank of Canada will continue to sound more dovish than the Fed."
Statistics Canada said the surplus came as merchandise imports fell 1.5 per cent in September, while exports rose 1.1 per cent.
Imports slipped to $44.1 billion, as volumes were down 1.0 per cent and prices were down 0.6 per cent.
The drop came as imports of energy products dropped 19.4 per cent, due in large part to lower crude oil and crude bitumen imports which fell 36.4 per cent as some Canadian refineries underwent maintenance work.
Exports, however, rose to $44.8 billion, as volumes were up 1.6 per cent and prices fell 0.4 per cent.
Statistics Canada said exports of motor vehicles and parts increased six per cent in September.
Imports from the United States rose 0.7 per cent to $29.7 billion in September, while exports were up 0.8 per cent to $33.7 billion, leaving Canada's trade surplus with that country virtually unchanged from August to September at $3.9 billion.
Exports to other countries increased 2.1 per cent to $11.1 billion and imports fell 5.8 per cent to $14.3 billion, shrinking the that trade deficit to $3.2 billion in September from $4.3 billion in August.