Michael Baldisimo added his first career MLS goal and assist in his second MLS start for Vancouver, which snapped the Whitecaps' stretch of 306 scoreless minutes in league play and 396 scoreless minutes across all competitions.
Thomas Hasal made seven saves for the Whitecaps, who were outshot 22-7 overall and 9-3 in efforts on target by a Toronto side that beat them twice at BMO Field last month.
Alejandro Pozuelo scored his third goal and contributed his eighth assist for Toronto, which twice erased a one-goal deficit prior to Nerwinski's match-winning goal.
Jonathan Osorio also scored for the visitors, who have lost two consecutive games for the first time since May of 2019 after having an 18-match unbeaten run snapped by Montreal earlier this week.
The Whitecaps scored two of their goals from set pieces, including Nerwinski's winner that came from Ali Adnan's free kick from the left.
From the restart, Adnan crossed the ball beyond the back post to the right side of the penalty area, where Andy Rose reached it and sent a low cross back across the goalmouth. Nerwinski met it there, driving a low, first-time effort past Toronto goalkeeper Quentin Westberg for his second goal of the season.
Earlier in the second half, it was Baldisimo who scored to give Vancouver a 57th-minute lead after a set-piece opportunity.
Adnan drove an initial free kick from just beyond the penalty area into Toronto's defensive wall. The redirection came to Baldisimo, who controlled it with his first touch and ripped a right-footed strike past Westberg's dive and inside the left post with his second.
Toronto leveled the match for a second time in the 71st minute, when Pablo Piatti curled an in-swinging ball toward the back post. Pozuelo slipped away from Nerwinski and met the cross with a first-time header past Hasal.