The Argentina forward was ruled out of Thursday's 3-0 win over Guangzhou Evergrande at the last minute because the club said he was suffering from renal colic, a condition associated with kidney stones.
The sports daily AS said on its website that Messi had endured another "bad night" but had passed the stone which was causing him pain. The club said he had missed training on Friday but did not give any further details.
Messi is battling to be fit for Sunday's final against River Plate, which would be only the second time in his career that he has played against an Argentine team.
Brazilian forward Neymar also missed Thursday's match after suffering a small strain in an adductor muscle before a Champions League match against Bayer Leverkusen last week. Barca said he continued rehabilitation work.
Barca are runaway favourites to win the tournament for a third time since it started in 2005.
(Writing by Brian Homewood; editing by Justin Palmer)
