Murray, a finalist in Metz in 2007, fell a set behind when Humbert seized his first opportunity with a flashing stop-volley to break for a 5-4 advantage, then served out for the set.
Murray, who swapped shirts while seated on his changeover bench before the final set, is among those who have advocated for some sort of rule switch.
In the five hours contest, Murray did not appreciate that Tsitsipas took a medical timeout after third set and made lengthy visit to locker room after fourth.
Stefanos Tsitsipas will aim to begin his quest for a maiden Grand Slam when he takes on former champion Andy Murray.
Andy Murray has been battling injuries of late, including a groin problem that has limited his time on the court this season.
Murray was initially scheduled to face Kyrgios but the Aussie withdrew just before the start of their match, throwing Sunday's schedule into chaos.
Andy Murray made good on a main draw wildcard to win his opening game against Richard Gasquet at the Western & Southern Open.
2012 US Open champion Murray was the first player on the alternate list after he missed out on the initial main draw field in July.
Spain's Sara Sorribes Tormo defeated Barty 6-4, 6-3 in straight sets to enter the next round. The entire match lasted for one hour and 34 minutes.
"There is a part of me that feels a bit like I have put in so much work the last three months and, ultimately, didn't play how I would want and expect. And it's like: Is it worth it?" Murray said.
Andy Murray was disappointed after winning just eight games against Denis Shapovalov in the third round at Wimbledon.
The 34-year-old Murray recently returned to the tour after a three-month absence because of a groin problem, just the latest in a series of injuries.
All week at the All England Club, nurses, health staff as well as the developers of coronavirus vaccines have been honoured in the Royal Box on Centre Court.
In his first singles match at Wimbledon in four years, Andy Murray defeated Nikoloz Basilashvili 6-4, 6-3, 5-7, 6-3 at the Centre Court.
Murray, the champion in 2013 and 2016 but who has fought a long battle with hip and groin injuries in recent years, triumphed 6-4, 6-3, 5-7, 6-3 over the 24th seeded Basilashvili.