A run of 58 saw Wilson take the first frame but two-time world champion Williams replied with breaks of 68 and 86 to take frames two and three.
However Wilson replied in kind compiling runs of 91, 95 and 69 to take three of the next four frames but Williams claimed a tactical eighth frame to send the match to a decider.
Wilson, who overcame Ronnie O’Sullivan in round four, claimed the ninth frame to make the semi-final stage.
Earlier, Barry Hawkins overcame Michael White 5-2 to also make the semi-final stage.
Hawkins claimed three of the first four frames to go to the interval with a healthy 3-1 advantage and, while White rallied briefly, runs of 60 and 70 saw the world number 14 into the next round.
Meanwhile, Anthony Hamilton overcame Mark Allen 5-2 to set up a semi-final against Hawkins.
Breaks of 96 and 78 helped Hamilton advance to a commanding 3-0 lead, before Allen fought back thanks to a steady 72.
Allen had the chance to reduce the deficit to 4-3, but a missed black on its spot allowed Hamilton to swoop in and steal the frame and the match.
Northern Ireland Open quarter-final results
Kyren Wilson 5 – 4 Mark J Williams
Barry Hawkins 5 – 2 Michael White
Anthony Hamilton 5 – 2 Mark Allen