The 19-year-old winger reported back after the deadline following England’s recent Euro 2020 qualifiers, and was handed an £86,000 fine and ordered to train alone in the pouring rain.
Dortmund boss Lucien Favre is said to have been angry with Sancho for returning almost 24 hours late, with this not the first instance of his punctuality causing problems.
The club’s sporting director, Michael Zorc, said there was “no alternative” but to punish the ex-Man City youngster, who earns a salary of around £5.2 million.
Zorc said: “Jadon is a decent boy. He is still very young. We did not make the decision easy, but it was no alternative.
“The suspension is only valid for today.”
Sancho was also dropped for their clash with Bundesliga leaders Borussia Monchengladbach on Saturday, although they managed to secure a 1-0 win without him.
England landed back at Birmingham airport at 4am on Tuesday, with a car waiting for Sancho to take him to London to see his family, before going back to Germany.
Favre said on Thursday: “The expectations of Jadon are enormous, but that is dangerous.
“Jadon is a great player, no discussions, but he still has a lot to learn.”
The FIFA Golden Boy nominee has been in good form this season, scoring four times in 11 appearances for his club, as well as notching twice for England in the win over Kosovo.
A number of clubs are now showing an increased interest in signing him, with Man Utd ready to battle Real Madrid for his signature next summer, while Liverpool boss Jurgen Klopp is also a keen admirer.
Borussia Dortmund assistant manager Jorg Heinrich recently conceded that Sancho could be gone within the next couple of seasons.
“Jadon can become one of the best players in Europe, or even the world,” Heinrich told Omnisport .
“It won’t be easy to keep him at Dortmund. We hope he plays one or two seasons longer but we all know very, very big clubs with a lot of money want to have him in their team.
“He should know Dortmund is an excellent place for young players to play consistently and to develop on a very, very high level.”