Dispy Selolwane scored twice and assisted on the 90th-minute Chris Armas goal that decided the series.
The Fire scored its four goals after the 36th minute ejection of San Juan Jabloteh's Ian Gray.
Gray was ejected for a late shoulder challenge on Nate Jaqua that sent him into the Soldier Field wall and onto the concrete that rings the field.
2003 MLS rookie of the year Damani Ralph opened the scoring with an assist from fellow Jamaican Andy Williams.
Selolwane's first goal came on a 25-yard shot and he finished his second after taking a Ralph pass and dribbling around keeper Daurance Williams.
Selolwane's through ball in the 90th minute set up Armas' decider.
Chicago will meet Costa Rica's Saprissa in a semifinal series April 14 and 21.