The Briton had opened the tournament with a bang on Tuesday when she shocked 23-times grand slam champion Serena Williams 6-1 6-0, the worst loss of the American great's career.
Konta was unable to recreate the magic, however, instead squandering a 5-2 lead in the opening set against the Belgian before bowing out meekly.
Mertens, bidding for her fourth title of the year, moves into a semi-final against fifth seeded Romanian Mihaela Buzarnescu.
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American Danielle Collins also moved into the semis after former world number one Victoria Azarenka retired injured when trailing 3-0 in the second set after claiming the first in a tiebreaker.
Venus Williams suffered an upset 6-4 7-6(2) defeat at the hands of Greece’s Maria Sakkari. The 38-year-old Williams held a 3-0 lead in the opening set and was up 5-3 in the second but could not hold off a relentless opponent 15 years her junior.
Williams has not advanced past the third round of a tournament since March and has yet to find the form that helped her reach two Grand Slam finals in 2017. World No. 49 Sakkari has moved through her first three matches without dropping a set. She needed one hour and 43 minutes to beat Williams, and saved two set points in the second set in the process.
Elsewhere, unseeded German Andrea Petkovic reached the Citi Open semi-finals for the second consecutive year, beating sixth seed Belinda Bencic 6-3 2-6 7-6(8) on Friday.
The 2013 runner-up rallied from a set down to defeat second seed Sloane Stephens on Thursday, and continued her momentum at the Washington DC event.
"I thought I was really solid throughout the whole match," Petkovic told reporters. "She played really well in the second set and then in the third set, it was just a momentum swing, up-and-down and emotions. I just tried to stay in the moment and within myself, and do the things I needed to do."
In the nail-biting tiebreak, Petkovic led 5-2 but had to save three match points before converting her first to seal her spot in the final four.
The 30-year-old will next face the winner of the match between eighth seed Yulia Putintseva and Svetlana Kuznetsova. The two competitors had their match delayed by rain with Kuznetsova having won the opening set and the second set tied 2-2.
Seven seed Croatian Donna Vekic was leading 3-0 over Magda Linette in the opening set when play was suspended. China’s Saisai Zheng had her match against American Allie Kiick postponed until Saturday.
Australian Open
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