Selt, from Romford, had let a 9-4 lead slip in their Sunday clash but he managed to recover to win 10-9 and earn a Crucible debut.
The 28-year-old world number 45 led 6-3 after the first session before extending to 9-4 with breaks of 62 and 67.
But 1997 world champion Doherty nailed a 128 as he launched a stirring fightback that saw him level at 9-9.
Selt regained his composure for the decider to close out a win that puts him in Monday’s random draw.
"Even at 6-3 I knew it would be tough today," said Selt. "From 9-4 Ken started to play well and when I missed the chance to win 10-7 I started to feel edgy.
“But when it went to a decider the pressure was reversed and I felt very calm.”
Mark Davis ousted China's Liang Wenbo 10-6 after winning five of the last six frames with top breaks of 115, 61, 65 and 103.
Davis, the world number 16, would ordinarily have skipped qualifying but was relegated from automatic seedings following the return of Ronnie O’Sullivan.
O’Sullivan is the defending champion but, after a self-enforced break from the sport, slid to world number 28, meaning only the top 15 qualify by rights this season.
Scotland’s Alan McManus, meanwhile, will return to the Crucible after a seven-year absence after he beat Tom Ford 10-5.
Jimmy White will not be present in Sheffield though after he lost 10-5 to Robert Milkins in the evening session, while Martin Gould is through after getting the better of Rod Lawler 10-7.
Peter Ebdon also qualified after winning a marathon match against Lewisham-born Norwegian Kurt Maflin 10-8, while Mark King denied Yu Delu his Crucible debut, defeating the Chinese player 10-9.
World Championship qualifying results (Sunday):
Matthew Selt 10-9 Ken Doherty
Mark Davis 10-5 Liang Wenbo
Alan McManus 10-5 Tom Ford
Robert Milkins 10-5 Jimmy White
Mark King 10-9 Yu Delu
Marcus Campbell 10-4 Liam Highfield
Dominic Dale 10-5 Alfie Burden
Sam Baird 10-3 Joe Perry
Martin Gould 10-7 Rod Lawler
Peter Ebdon 10-8 Kurt Maflin