The news was confirmed by the Germany team's Twitter account in a tweet that read: "The game has ended 5 minutes early with the score at 1-1. The Germany players left the pitch after Jordan Torunarigha was racially abused."
The Honduras Football Federation said on their Twitter page: "Game ended in the 87th [minute] due to abandonment because of a German player alleging a racist insult from a Honduras team member. Regarding this matter, the Honduras Football Federation states that the situation was a misunderstanding on the pitch."
The statement added: "The Honduras FA reaffirms its faithful commitment to fighting against racial or ethnic discrimination following national and football principles. Honduras is multi-racial and inclusive national and our Olympic team reflects and celebrates this diversity...our national players do not engage or have had any kind of relationship with any practice of racial segregation and are firmly committed to stand in solidarity with movements promoting equality and racial justice as a fundamental principle of our nation."
"If one of our players is racially abused, it's not an option for us to keep playing," Germany coach Stefan Kuntz said. "It was hard to get him in, he was terribly upset because he said he was repeatedly racially abused. For us it's clear, this violates our values, we cannot tolerate it. We'll take our player completely under our protection."
Torunarigha's club, Hertha Berlin, responded by saying "that's the only correct decision!"
"After the situation calmed down a bit, the whole Honduras team came over to us on the bench and apologised," Kuntz said. "That was the end of the matter for us."
Germany captain Maximilian Arnold said the team discussed taking the matter further but decided against it.
"We made a correct statement, we made the right decisions and acted correctly. It was also Jordan's wish. He said that we should leave it at that," Arnold said.
The behind-closed-doors warm-up game was arranged to prepare for the Olympic Games and took place in Wakayama, Japan.
The German football association confirmed the game was played in thirds of 30 minutes with Douglas Martinez scoring for Honduras in the 21st minute.
Felix Uduokhai equalised for Germany in the 84th minute, but Germany left the pitch soon after.
Torunarigha, 23, is a defender who plays for Hertha Berlin in the German Bundesliga. He has represented Germany throughout the age groups from under-16 level to U21.
The friendly game in Wakayama, Japan was Germany's last preparation match before it plays Brazil in Yokohama on Thursday. Kuntz' team also plays Saudi Arabia on July 25 and Ivory Coast on July 28 in Group D.
Information from the Associated Press was used in this report.