The British number one looked on course for victory as she served for the match, but let two match points slip by, allowing Makarova to take the win 5-7 7-6 (7/4) 6-3.
Konta, who reached the quarter-finals on her Rogers Cup debut last year, was behind 4-2 in the first set but hit back to level it a 4-4, before breaking her opponent again to edge in front.
Makarova, ranked 42 in the world, went a break up early in the second set, but Konta recovered to win the next four games to lead 5-2.
But when serving for the match, Konta failed to take the opportunity as she misjudged a forehand which went long, and Makarova broke back.
Konta then had another match point in the next game but again she could not make it count as the Russian pulled back to 5-5 and then clinched the tie-break to take the match to a deciding set.
The third set remained on serve until Makarova broke to go 5-3 up, and despite Konta saving the first match point, she could not do the same with the second and crashed out early.