Jones was withdrawn in pain in the eighth minute of the first-ever Lions Test in Scotland on Sunday (AEST) with a shoulder dislocation that was later ruled bad enough to rule him out of the South Africa tour entirely.
Justin Tipuric was also forced off with an injury in the first half of the Lions' first meeting with Japan ahead of the tour of South Africa, which Warren Gatland's side won comfortably to lift the 1888 Cup.
Josh Adams, Duhan van der Merwe and Tadhg Beirne marked their debuts with a try, while Robbie Henshaw also touched down and the excellent Dan Biggar was on target with all four conversions.
Japan, playing its first Test since losing to the Springboks in the quarter-finals of the 2019 Rugby World Cup, entertained in the second half and was rewarded with a try from Kazuki Himeno.
There was concern for the Lions when skipper Jones was replaced early on after doing damage while trying to turn the ball over before his Wales team-mate Adams got the first points on the board.
The winger showed great feet and good strength to come in off the line and power his way over after a strong run from Bundee Aki.
Tipuric also made a concerning early exit before Van der Merwe caught Japan napping, picking the ball up from the back of a ruck and crossing all too easily.
The Lions were dominant and Ireland centre Henshaw ploughed over from close range after taking a pass from Conor Murray, with the impressive Biggar's third successful conversion increasing the lead to 21-0.
Courtney Lawes, Jones's replacement, lost control before grounding the ball when he crashed over early in the second half, but Beirne took a great line and showed a sharp turn of foot to burst through and go under the posts.
The Brave Blossoms enjoyed themselves after the break and Himeno finished after a lineout routine as the Lions defence work given a great workout with bigger tests to come.