Dominique Görlitz, an amateur archaeologist, was sentenced to a five-year prison term by a court in Giza, south of Cairo, on Tuesday evening along with two colleagues and their Egyptian assistants.
Judges found that Görlitz and his colleague, author Stefan Erdmann, had illegally taken artifacts from the pyramid, and brought them back to Germany.
Pieces of a scroll bearing the name of the Pharaoh Khufu and rock samples had been removed, the court found.
The Great Pyramid, also known as the Cheops Pyramid, was built around 2600 BCE for the Pharaoh Cheops. It contains Khufu's tomb and is the only remaining wonder of the ancient world.
The Germans had to be tried in absentia as they had long since left for their home country, but the six Egyptian accomplices including three Antiquities Ministry employees, two pyramid guards, and a travel agent were taken straight to jail.
A judicial source told AFP that the court had also ordered an inquiry into former Antiquities Minister Zahi Hawass. Hawass called the report "totally unfounded".
In a post on his Facebook page on Wednesday, Görlitz wrote that the Cairo judgement was "an incomprehensible shock for all the accused."
"I want to clarify once again that we neither damaged the Cheops pyramid, nor did we steal artifacts," he said.
The archaeologist claims that he took "milligram-scale samples" from paint on the walls of the royal tomb and later offered to return them to the Egyptian Antiquities Ministry.
He added that the defence lawyers did not have access to the charges against their clients and that the Antiquities officials were punished although they had done nothing more than visit a separate archaeological site with the Germans on the same day.
Meanwhile, state prosecutors in Görlitz's home town of Chemnitz are pursuing him for a fine of several thousand Euros for theft and property damage for the same alleged crime.
"The judge will now have to examine what influence the [Egyptian] ruling will have," a spokesman for the civil court in Chemnitz said.
Görlitz is challenging the prosecutors' allegations and the case will be decided on in February next year.
Although he does not contest the fact that he took the samples, Görlitz argues that his actions did not constitute a crime.