Toronto dominated a lopsided first half, but wasn't clinical enough in front of goal and saw Sean Johnson make a number of great saves in the NYCFC goal as the two teams went to the dressing room locked in a goalless draw.
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The narrative changed after the break, though, with Toronto getting a deserved opener when a horribly misplaced clearance fell to Pozuelo and he buried his shot past Johnson.
That opener seemed to enliven Domenec Torrent's side and the NYCFC pressure finally paid off as Maxi Moralez found Ismael Tajouri-Shradi with a cross to the back post and he smashed a superb first-time shot into the back of the net.
Pozuelo then converted from the penalty spot late in the second half after a horrendous challenge byRonald Matarrita in the box to seal the win for the 2017 MLS Cup champions.
TFC, who now awaits the winner of the match between Atlanta United and the Philadelphia Union, defeated D.C. United 5-1 in extra time in its first-round playoff game on Saturday while NYCFC enjoyed a first-round bye.
Top seed NYCFC knocked out by Toronto's late penalty
Alejandro Pozuelo's 90th-minute Panenka kick sends Toronto to the conference final. Watch MLS on ESPN+.