The 19-year-old Magno, who scored only twice in the regular season, helped NYCFC defeat Philadelphia in the Eastern Conference final on a day the visitors were without MLS Golden Boot winner Valentin Castellanos due to a red-card suspension. Castellanos will be able to return for Saturday's final against the Portland Timbers.
Maxi Moralez also scored for fourth-seeded City, who prevailed over the East's No. 2 seed Philadelphia after advancing past Supporters' Shield winners and top-seeded New England Revolution on penalties in the conference semifinals.
COVID-19 protocols ruled 11 players out for the hosts, who were forced to make six changes from the starting lineup of their previous-round triumph on penalties over No. 3 seed Nashville City SC.
Union leading scorer Kacper Przybylko helped pressure NYCFC into an own goal to give Philadelphia a lead that lasted less than two minutes.
Only seconds after the restart following Philadelphia's 63rd-minute goal, New York's Maxime Chanot drove a speculative effort from distance that wrong-footed third-choice goalkeeper Matt Freese into an awkward save. Magno got a piece of the rebound before it eventually fell to Moralez at the back post, who hammered a powerful finish past Freese.
Instead, minutes later Gudmundur Thorarinsson seized upon a mistake from defender Olivier Mbaizo to work free inside the left side of the penalty area. From there, he drove a firm cross to the sprinting Magno, who hammered a first-time finish past Freese.
NYCFC, in their seventh season of existence, will now travel to Portland for a title-deciding date with the Timbers at Providence Park on Saturday (3 p.m. ET, stream live on ABC).