The ckub have confirmed the nature of the injury and have said the player will have scans on Sunday.
Dembele was playing as he attempted to return from another hamstring problem that saw him miss a month of action between March and April.
Barcelona lead the tie 3-0 after the first leg.
Dembele has had a stop-start campaign already this year and only managed 24 appearances last season, his first at Camp Nou.
He has managed 43 games in all competitions for the Blaugrana this year, scoring 14 goals, but has missed time with a sprained ankle in addition to the hamstring injury.
❗ [BREAKING NEWS] O.Dembélé has a hamstring injury in his right leg. He'll undergo tests tomorrow to determine the exact extent of the injury. pic.twitter.com/q3Ze4JijJE— FC Barcelona (@FCBarcelona) May 4, 2019
On his return from injury in April his coach, Ernesto Valverde, said his team would be cautious about the pacy 21-year old.
“He’s not exactly the same as before his injury,” Valverde said.
“You have to go through games before finding your place. We’ll see.”
“He definitely offers us speed and if other teams play high he’s great on the counter. We can exploit that.
“He’s very good in one-on-ones as well.”
Dembele was signed by the Catalans from Dortmund for €105m (£89.4m/$117.7m) in the summer of 2017, and was seen as a replacement for Neymar, who left for PSG the same summer.
Despite the spluttering nature of his start to his career in Spain, club president Josep Bartomeu insisted he was already a better player than the Brazilian.
“We are happy with what we have as Dembele is better than Neymar and he is a good professional player,” Bartomeu said in April.
“He is a young guy who arrived at a huge club and that’s not easy, but he has adapted and he is much better than Neymar.”
Barcelona have already clinched their second consecutive La Liga crown and were fielding an experimental side against Celta, who started the game just two points above the relegation zone.
Dembele was replaced by 20-year-old Alex Collado, who is making his debut for the first team.