Spurs fans were hurt as they struggled to enter the Westfalenstadion before the last-16 game, with entrances temporarily closed.
Dortmund police used pepper spray to try to control the Spurs fans.
Uefa's disciplinary body has charged Dortmund with blocking stairways and will hear the case on 19 May.
The congestion developed as supporters were redirected by police towards a different entrance into the stadium shortly before kick-off.
Tottenham say this created "a potentially dangerous situation" and condemned the use of pepper spray as "unnecessary and unacceptable".
Dortmund police said the late arrival of Spurs fans had created unexpected pressure on the entrances, which had to be temporarily closed.
Martin Cloake, co-chairman of the Tottenham Hotspur Supporters' Trust, told the Press Association: "It's one of the worst experiences I've had to get into a ground."
Spurs lost the game 3-0, with the second leg to be played at White Hart Lane on Thursday.
Borussia Dortmund have been charged by Uefa after 17 Tottenham fans were injured before last week's Europa League first leg match.