The 6-foot-6 Argentinian, the 2009 U.S. Open champion, had only dropped 13 games in two matches before facing Chardy -- the fewest number of all the men -- until his 6-3, 6-3, 6-7 (3), 3-6, 6-3 third-round defeat.
Chardy won the first two sets and, after del Potro rallied to level at two-all, got the crucial break in the eighth game of the fifth set and then held to clinch the match, closing with an ace.
The 36th-ranked Frenchman frustrated del Potro with a mix of drop shots, well-angled forehands and backhand slices, one of which sent del Potro running into the stands in the third set.
"Of course, it's not a good result after I came back from two sets down, but Jeremy played really well in the fifth set," del Potro said. "He was so calm to close the match in the end.
"Jeremy played so strong during four hours. He made a lot of winners with the forehand, very good slices. In the end, when he had the chance to break me, he did. He played better in the important moments and he took the chance to win the match."
Second-seeded Roger Federer was the last of the main contenders to advance to the fourth round, beating Australian Bernard Tomic 6-4, 7-6 (5), 6-1. Federer trailed 4-1 in the tiebreaker but rallied for six of the next seven points in front of a full house at the 15,000-seat Rod Laver Arena.
"I had a few more chances than he did, but I thought the tiebreaker was going to go his way," said Federer. "I think overall we played a great match, he really got the best out of me tonight."
Del Potro had been tipped as an outside contender for the title in the absence of 11-time major winner Rafael Nadal, but his loss leaves only leaves three Grand Slam winners in the men's draw.
Chardy had a win over No. 3-ranked Murray at Cincinnati last year, but said the win over del Potro was a bigger personal achievement in the circumstances.
"Here it's something more because Australian Open, third round, I play a top player," he said. "It's a big win for me. And maybe the best of my career."
Murray, the reigning U.S. Open champion, advanced to the fourth round of a Grand Slam for the 19th consecutive time with a 6-3, 6-4, 7-5 win over Lithuanian qualifier Ricardas Berankis.
Murray began his streak of fourth round of better in Grand Slams at Wimbledon in 2008, after having lost in the third at the French Open a month earlier.
The 25-year-old Scot, who ended a 76-year drought for British men at the majors by winning the U.S. Open last year, has not dropped a set at this year's Australian Open. He will next play either Frenchmen Gilles Simon or Gael Monfils.
In other men's results, a pair of Frenchmen advanced and will meet in the fourth round, with No. 7 Jo-Wilfried Tsonga beating Slovenia's Blaz Kavcic 6-2, 6-1, 6-4 to set up a meeting with No. 9 Richard Gasquet, who fended off Croatia's Ivan Dodig 4-6, 6-3, 7-6 (2), 6-0.
Information from The Associated Press was used in this report.