Excelsior booked their place in the Eredivisie on Sunday and relegated city rivals Sparta Rotterdam in the process.
Guyon Fernandez had missed an 86th-minute penalty for visitors Excelsior, but turned from villain to hero with the decisive strike.
Rydell Poepon put Sparta ahead in the second minute of stoppage time, but 60 seconds later Fernandez struck to earn a 1-1 draw which secured Excelsior's promotion following the 0-0 draw in the first leg.
Willem II survived their relegation-promotion encounter with Go Ahead Eagles, winning the second leg 3-0 after extra-time for a 3-1 aggregate triumph.
Frank Demouge's 27th-minute strike put Willem II 1-0 up after 90 minutes and Mehmet Akgun scored after 99 and 115 minutes to ensure survival.