Sancho returned to training with Dortmund this weekend after recovering from a thigh injury which has kept him out since early March but is not expected to recover in time to face City.
The 21-year-old winger joined Dortmund from City in a £7m deal in 2017 in search of more first-team opportunities, having starred in the Etihad club's academy system.
The quarter-final draw offered the prospect of Sancho meeting his former employers for the first time but, having missed Dortmund's 2-1 first leg defeat last week, he will also sit out of the return leg at Signal Iduna Park.
"Jadon won’t be at our disposal although he is training again," said Edin Terzic, Dortmund's interim head coach. "He’s giving his best to return as quickly as possible.
"We would like to have him with us tomorrow but he can't. We have to take our time with him. He's not an option for tomorrow but we hope it won't last any longer."
Dortmund may also be missing captain Marco Reus and defender Mats Hummels, who were substituted during their 3-2 Bundesliga win away to Stuttgart on Saturday.
Reus scored the away goal at the Etihad in last week's first leg which gives Terzic and his players hope of turning the tie around and denying City passage to the semi-finals.
"There are a few players who are slightly injured. We have to wait," the Dortmund coach said.
"You saw what happened to Marco Reus and Mats Hummels. They needed to be substituted and leave the pitch on Saturday. We have another training unit tomorrow as well, then we will see who is at our disposal."
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