Trudeau said he would appoint Malcolm Rowe from Newfoundland and Labrador to fill the vacancy of a retiring Nova Scotia judge at the top court, which has nine justices.
Atlantic Canada - where Trudeau's Liberals won all of the 32 Parliamentary seats in an October 2015 election - has traditionally held one of the nine slots.
In August, Trudeau sparked anger in the region with comments that suggested it wouldn't be guaranteed a spot on the court.
Trial lawyers from Atlantic Canada announced they would challenge Ottawa in court if the position was filled by someone from another part of the country.
The official opposition Conservative Party said on Monday it was pleased to see Trudeau had stuck with tradition and appointed a judge from Atlantic Canada.
Rowe is the first top judge to be appointed under new rules which the government says are designed to make the process more accountable and ensure qualified candidates come from across Canada, rather than from one particular part of the country.
The selection of Supreme Court judges in Canada has traditionally been less political than in the United States, though there have been controversies.
In 2014, the Supreme Court rejected then-Prime Minister Stephen Harper's pick of Marc Nadon in a high-profile clash, saying the nominee was not qualified.
US Supreme Court appointments have become highly politicized. The nine-member US high court has had a vacancy since the death of Justice Antonin Scalia in February because the Republican-led Senate has refused to take any action on Democratic President Barack Obama's nominee to the position.