Soeren Eismann, who scored the goal, was surrounded by livid opponents and later said he did not realise what was happening.
SV Meppen were leading 2-0 away to Carl Zeiss Jena when the incident happened in the 57th minute.
Jena's Julian Guenther-Schmidt went down after a tackle and Meppen player Nico Granatowski, who was in possession, stopped and raised his hand, indicating he was going to put the ball out of play.
Jean's Eismann, however, took the ball off him and ran on to score.
The referee, who had not stopped play, awarded the goal, Eismann found himself surrounded by angry opponents and the protests held up the restart for almost five minutes.
In a further twist, Eismann scored again in the 82nd minute to give bottom-of-the-table Jena a 2-2 draw. There were further scuffles at the end of game, German media said.
"I can understand why they're angry but I didn't see that one of them was down," Eismann told German media.
Meppen coach Christian Neidhart said the incident left him "lost for words""
His opposite number Mark Zimmermann said: "I am not proud of this situation, even though I cannot assess it precisely because I was not on the field. This situation significantly influenced the game."
