Clarke converted a slick cross from Nichelle Prince with a deft left foot to break a scoreless deadlock at Tofig Bahramov Stadium.
The Richmond, B.C., striker later notched what looked to be an insurance marker as well, but she was ruled offside and the goal disallowed.
With the win, Canada vaulted over Colombia in the Group A standings with four points — same as front-running Nigeria, which clobbered host nation Azerbaijan 11-0.
Canada meets Azerbaijan in its final group-stage match on Saturday (CBC, CBCSports.ca, 11 a.m. ET).
The Colombians had opened the tournament in promising fashion with a 4-0 rout of Azerbaijan, but failed to generate much by way of offence against the hard-working Canadians.
Canada controlled the tempo for the most part and enjoyed the better scoring chances, especially in the first half.
Prince, from Ajax, Ont., failed to corral a bouncing ball in front of a gaping net and Valerie Sanderson of Boisbriand, Que., had a bounding left-footer smothered by Colombian keeper Lissa Cardozo.
Toronto's Rebecca Quinn nearly converted too, only to head the ball wide of the post off one of Canada's five corner kicks.
At the other end, Canadian keeper Kailen Sheridan was rarely tested as Canada outshot Colombia 16-8.
Sheridan, from Whitby, Ont., easily handled the most legitimate attempt by Las Cafeteras, a rising shot off the boot of Dayana Castillo with two minutes remaining.
Castillo, who tallied twice in Colombia's opening win, sailed a shot high over the crossbar earlier in the match.
Canadian kicked off the tournament with a 1-1 draw against Nigeria.
Montreal's Amandine Pierre-Louis staked Canada to a 1-0 lead in the 63rd minute of that match before Chinwendu Ihezuo replied in the 81st minutes for the Flamingoes.