The Brazilian, who helped set up their goal, was taken off injured three minutes after the restart with Gladbach conceding two goals to lose their second consecutive Group C match.
"A scan today revealed that the Brazilian sustained torn muscle fibre in his left thigh," the club said in a statement.
"So Raffael will not be available for Borussia for the coming period," it said, without specifying the length of his absence.
The 31-year-old had already missed their previous two league matches with an adductor muscle injury but the club said the new injury was unrelated.
Gladbach are fourth in the Bundesliga on 10 points, five off leaders Bayern Munich.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
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