The 41-year-old, who made his Grand Slam breakthrough at the Australian Open by winning the 2014 title before adding trophies at the French Open and the US Open in subsequent years, is set to end his storied playing career later this season.
He delighted fans with a run to the Melbourne third round earlier this year, but there was to be no extended farewell in Paris after lucky loser De Jong cruised through the first set and held his nerve to prevail after a mid-match blip.
"Thank you all. It's hard, I don't want to say goodbye to you here," Wawrinka said, before thanking tournament director Amelie Mauresmo and French Tennis Federation chief Gilles Moretton.
"It's thanks to tournaments like this one that I dreamed of becoming a tennis player. I grew up with the goal of competing here one day.
"It was an amazing experience to be able to share this moment here on court. Well done to Jesper for the match."
Fans on Court Simonne Mathieu chanted Wawrinka's name and cheered when he unleashed winners and erupted after the Swiss levelled the clash at one set apiece, but De Jong was soon on the front foot again.
The world number 106, who only advanced to the main draw after Frenchman Arthur Fils' withdrawal through injury, bagged the third set after an early arm-wrestle and delivered the knockout blow in a tight fourth set.
"It's not about me today," the 25-year-old De Jong said in a brief on-court interview.
"A funny story about Stan, he played my coach when I was a ball kid. I don't want to say he's old. But it's all about Stan today, especially the way he fought."
After a short video tribute played on the big screen, an emotional Wawrinka hailed fans for making his final appearance in Paris special.
"Three hours of emotion, three hours of battle thanks to you, thanks to the support you've given me all these years," Wawrinka added.
"I wanted to keep going, to go as far as possible until I was 41 to experience emotions like today. I've been lucky enough to experience them for a very long time. You never want to say goodbye when you're passionate about something.
"I know it was the end; I gave everything for this sport, and I know it's the right choice. I would have loved to be back here, in front of you, but unfortunately, this was my last match at Roland Garros."
A second tribute followed shortly afterwards, with Roger Federer, Rafa Nadal, Novak Djokovic, Carlos Alcaraz, Jannik Sinner and Gael Monfils all celebrating Wawrinka's career.