A police spokesman said the threat was made by email against the Hofburg, a sprawling palace complex that includes reception rooms, the headquarters of the Organization for Security and Cooperation in Europe (OSCE), and temporarily the debating chamber of Austria's lower house of parliament.
Police sealed off the area around Van der Bellen's office, including a square that separates it from the office of the head of Austria's government, conservative Chancellor Sebastian Kurz.
"The search was negative. All closures can be lifted!" the Vienna police said on Twitter on Wednesday evening.
Van der Bellen, a former leader of the left-wing Greens whose role is largely ceremonial, had been evacuated, a spokesman for his office confirmed, though he added that he did not know details of the threat or its target.
It remains unclear who made the threat or why.The part of the complex temporarily occupied by parliament while its main building nearby is being renovated was not evacuated, a parliament spokesman said. That area is at the opposite end of the palace.