"It's one of those things you've got to put behind you and move on as quickly as you can."
Gatland said he will name a replacement lock and captain later Saturday.
Flanker Justin Tipuric also left the match after being hurt in a ruck in the 21st minute. He suffered a stinger, Gatland. He will be scanned, but they were confident he will be OK.
The injuries blighted what was otherwise a good tour warmup for the Lions in front of their first and last crowd, a limited 16,500. All eight games in South Africa will be without spectators.
Jones played every test of the previous three tours and is the world record holder for test caps.
Tipuric's injury, and a later hamstring issue for No. 8 Jack Conan meant the Lions were down three loose forwards after Hamish Watson was concussed in training midweek. Also, tighthead prop Zander Fageron was withdrawn from the starting XV after a back spasm.
In Jones' absence, Lions veterans stepped up and the lineout didn't miss a beat. Lineout takes by Iain Henderson launched two first-half tries, and hooker Ken Owens, man-of-the-match flyhalf Dan Biggar and center Robbie Henshaw pulled the strings.
Just five minutes after Jones departed, midfielder Bundee Aki sliced through off lineout ball and right wing Josh Adams stepped two defenders and reached out to score the first try.
From an intercept by Henshaw, the Lions worked the ball left and right, and Duhan van der Merwe, off his left wing, took ruck ball to the tryline without a defender in sight. Biggar converted both tries from the right sideline.
From another Henderson lineout take, Henshaw burst off the ruck pass and scored.
Japan, playing the Lions for the first time, was full of energy but not accuracy, and the Lions defence upheld the 21-0 lead into halftime.
Courtney Lawes, who replaced Alun Wyn Jones, missed a try to start the new half when he lost control trying to ground it, but minutes later flanker Tadhg Beirne screamed over between the posts after a great pass from Biggar.
Japan finally got over the tryline it had been threatening, after replacement loosie Kazuki Himeno ran over Lions forwards Taulupe Faletau and Jamie George.
The Lions were left to play the last 10 minutes with 14 men after Conan went off and the bench had been cleared. Gatland said they pulled Conan because they didn't want another bad injury.
The Lions came under severe pressure from Japan. Himeno was denied a second try when he was held up by Henderson and Beirne, and a crosskick into the Lions in goal was barely defused by Anthony Watson.
The Japanese were enthusiastic and clever but well contained by the Lions. Japan plays Ireland next weekend, when the Lions will be playing their namesake Lions in their tour opener in Johannesburg.
