Gül eventually gave an abridged version of his speech two hours later, to a limited audience.
"There are people who wanted to delay this event," he said, "and when they heard that I still wanted to hold the speech, they made a bomb threat."
"We will never submit to terror," he said. "Any organization that makes a bomb threat is a terror organization."
police spokesman Michael Gassen said the threat had been taken seriously, even though the telephoned warning had been difficult to understand.
At the start of his speech, Gül said Roj television, a Kurdish station, had been urging viewers all day to disrupt his visit to the university, on the Unter den Linden avenue.
Opposite the building, some 50 demonstrators chanted and waved banners in support of the PKK
terrorist organization and its jailed leader, Abdullah Öcalan.
Slight scuffles broke out as police struggled to contain a throng of people trying to enter the building to listen to the speech after the alert was called off.