Hassan Yussuff defeated incumbent Ken Georgetti by 40 votes —2,318 compared with 2,278 for Georgetti.
There were 29 spoiled ballots in the hotly contested election.
Georgetti, who was born in Trail, B.C., was first elected in 1999 and went on to become the labour group's longest-serving president.
Yussuff was the CLC's secretary-treasurer and had held the position since 2002.
The labour organization said on its website that Yussuff was also the first person of colour to be elected to an executive position.
That happened in 1999 when he was elected an executive vice-president.
In the past, Yussuff, who was born in Guyana, South America, also co-chaired the CLC's human rights committee.
Barb Byers was elected to replace Yussuff as secretary-treasurer. She defeated Nathalie Stringer.
Byers, who's from Saskatchewan, was previously one of the CLC's two executive vice-presidents.
The Canadian Labour Congress, which represents 3.3 million workers, brings together national and international unions as well as provincial and territorial federations of labour and 111 district labour councils.