Paris Saint-Germain also goes through despite its 2-1 loss at City after leading when Kylian Mbappé scored early in the second half.
Following setbacks with a rehab procedure, he couldn't predict with certainty when Reyna would be able to train with the Dortmund team, or even if that would happen this year.
Hummels has said he expects to be suspended for their next Champions League game against Sporting Lisbon on November 24 which could be decisive in Dortmund's chances of making the last 16.
Despite a first-half red card, Dortmund led the game until Dusan Tadic leveled the score for Ajax in the 72nd minute, before goals from Sébastien Haller and Davy Klaassen gave Ajax the win.
The Ivory Coast forward scored four goals against Sporting Lisbon on his stunning Champions League debut last month, then also hit the target against Besiktas.
A look at what’s happening in European football on Tuesday
Victory sent Dortmund top of the table, leapfrogging Bayern Munich and Bayer Leverkusen, who meet on Sunday.
Haaland has scored 66 goals in 66 games for Dortmund, but a release clause in his contract becomes active next year, meaning he could leave for 75 million euros ($88 million).
Both teams already had — along with Bayern Munich — the best attacks in the league (nine goals from three games).
German Super Cup: Robert Lewandowski, Thomas Mueller on target as Bayern Munich beat Borussia Dortmund
New coach Julian Nagelsmann has earned a trophy, which Bayern also won last year against Dortmund in Munich, with his first win in charge.
Bayern Munich are bidding to win a tenth straight Bundesliga title, but were held to a 1-1 draw at Moenchengladbach last Friday.
The 21-year-old set up three goals and scored two after starting the season with a hat trick in the German Cup last weekend.
Dortmund compensated for the departure of Jadon Sancho to Manchester United by signing Donyell Malen from PSV Eindhoven.
Sancho, 21, is set to leave Dortmund, who have agreed a transfer with Premier League giants Manchester United.
The club said in a brief statement that the signing was "subject to contractual terms and a medical, which will be completed after Jadon’s involvement in the UEFA European Championship".