And, after undergoing preliminary medical evaluations after full-time, early indications make grim reading for the Bundesliga side.
"It is probably a muscle rupture," Dortmund sporting director Michael Zorc told reporters after the game.
Reus is now certain to miss Wednesday's return clash at Signal Iduna Park, as Dortmund seek to revert their tie against Benfica.
"This is sad news, he's been playing at a high level for weeks," coach Thomas Tuchel said as he confirmed Reus' absence midweek.
"That is a huge loss for us that definitely blurs this victory."
Dortmund went down in February's last 16 first leg in Lisbon, and must win by at least two goals to assure their place in the quarter finals.
It is currently unclear how much time Reus will miss in total, as Dortmund await the final medical evaluation on what appears to be a serious muscle injury.