The 1997 world champion kept alive his professional snooker career with victory against Fraser Patrick on Friday, but this meeting with King proved a step too far for the 50-year-old.
Doherty was 3-1 down at the mid session interval after a 125 break from his Romford rival, but the Irishman fought back with a break of 80 in frame six before he won frame seven as well.
King's class told in the end though and he came through to set up a meeting with Ian Burns on Tuesday.
A win for King will book him a return to the World Championship for the first time since 2013.
For Doherty, it could be the end of the road for his professional career unless he is handed an invitational tour card.
He had hoped to make it back to the Crucible again after last appearing at the Sheffield venue in 2014 when he stunned Stuart Bingham in the opening round before losing to Alan McManus.
Doherty's greatest triumph came in 1997 when he beat Stephen Hendry to win the World Championship, but he will not be back there this year.
Earlier in the day it was confirmed of the 202 tests carried out on players, officials and staff at the qualifying event, they all returned negative for Covid-19.
