The coach of the Bundesliga holders believes with hindsight he should not have played the defender, who tore ankle ligaments in the Revierderby prior to suffering from a virus
The Germany international had just spent 10 days on the sidelines with the flu, and was partly responsible for their fiercest rivals' first goal before being sacrificed at half-time.
However, Hummels also suffered torn ankle ligaments in the clash which could keep him out until mid-May, meaning he would miss the Champions League quarter-finals which will be drawn this Friday.
“Ideally Hummels would have been sat at home or with a doctor. It is true that Schalke got the chance because Mats could not walk properly,“ Klopp told Bild.
The Dortmund coach was also criticised for leaving Marco Reus out of the starting XI with Kevin Grosskreutz taking his place.
He added: "I had to make a decision and I would make it again. You take risks and are not always lucky. Our problems were in defence; Marco would not have helped us there."