The 35-year-old Jones, the Lions' talismanic captain and the most-capped Test player of all time, left the field in the seventh minute, and he was joined in the sheds not long after by the experienced Justin Tipuric.
Lions head coach Warren Gatland revealed afterwards Jones had suffered a dislocated shoulder and hinted that he will have to be replaced in the squad for the Castle Lager Lions Series.
Welsh speedster Josh Adams scored the opening try on his Lions debut to kick start the 2021 Tour in style after Warren Gatland’s men weathered an early storm from the Brave Blossoms.
SA-born Duhan van der Merwe, who made his Test debut at wing for Scotland in October 2020, joined the try-scoring debutant party shortly after before Ireland's Robbie Henshaw (centre) claimed the Lions’ third to give the Lions a comfortable 21-0 lead at the break.
Experienced England lock Courtney Lawes had a try ruled out after the restart but Irish loose forward Tadhg Beirne became the third player to score on debut on 49 minutes, with Wales flyhalf Dan Bigger kicking all four conversions.
Japan responded with their first try 10 minutes later as Kazuki Himeno found a gap off the back of a lineout while Yu Tamura cut the deficit further with a penalty on 69 minutes.
But despite the visitors fighting until the final whistle, nothing could stop the Lions from making a winning start to the Tour.
While the Lions’ intensity waned in the final quarter of the game, they still managed to keep out Kotaro Matsushima as Japan continued to probe the Lions in the closing stages.
Ultimately, it was a winning start for Gatland’s men and apart from the injury concerns, the Lions will fly out to South Africa with momentum on their side.
British & Irish Lions 28 (21) - Tries: Josh Adams, Duhan van der Merwe, Robbie Henshaw, Tadhg Beirne. Conversions: Dan Biggar (4).
Japan 10 (0) - Try: Kazuki Himeno. Conversion: Yu Tamura. Penalty goal: Tamura.