The British No. 1 served for a straight-sets win in the second-round contest but eventually fell 5-7 7-6 (7/4) 6-3 to the world No. 42 in almost two-and-a-half hours.
Seventh seed Konta battled back from a break down in the first two sets but could not recover after dropping her serve in the eighth game of the decider in Toronto. Konta trailed 4-2 in the first but hit back to level at 4-4, before breaking to love to take the set.
Makarova went a break up early in the second set following a Konta double fault, but the Briton recovered to win the next four games to lead 5-2. But when serving for the match, Konta sent a forehand long at 40-30 up and Makarova broke back.
Konta could not convert another match point in the next game as the Russian pulled back to 5-5 and then clinched the tie-break to force a decider.
The third remained on serve, without a single break point, until Makarova broke to go 5-3 up. And despite Konta saving the first match point, she sent her return of serve long when facing the second as she made an early exit from the competition.