Dembele was surprisingly handed a place in the team at the expense of Antoine Griezmann but only managed 25 minutes of the Group F clash at Camp Nou.
The France forward appeared to hurt his left ankle in an innocuous challenge with a Dortmund defender and had to be taken off by coach Ernesto Valverde.
Griezmann was introduced for Dembele with Barca soon opening the scoring through Luis Suarez.
Dembele has struggled for form and fitness so far this season, scoring a single goal in five LaLiga appearances, while he has failed to find the net in four Champions League games.
Barca will secure qualification for the next round if they beat the out of form Bundesliga side.