Chek Lap Kok's south runway reopened yesterday after the last of the wreckage from the China Airlines jet was removed eight days after it crashed.
The debris was cleared by midnight on Sunday and the runway reopened after the Civil Aviation Department inspected repairs to the surface.
A Government Flying Services Jetstream was the first aircraft to take off from the runway at 9.46am, followed by a Malaysia Airlines Boeing 747 heading for Kuala Lumpur.
An Airport Authority spokesman said all outgoing flights would use the south runway and all incoming flights would use the north runway between 10am and 4.30pm each day.
After 4.30pm, all aircraft would take off and land at the south runway.
The spokesman said the practice was the same as the one in operation since late May when the second, or north runway, was opened.