The man, who police said was 40-years-old, was stopped by police after he drove his car with Heidelberg plates through barricades with screeching tyres at the memorial near Berlin's Tiergarten park and threw a bucket of red paint before the podium where Obama will speak.
The bomb squad checked the car for explosives, but quickly determined there was no danger posed by the vehicle.
"We don't yet know what his motives were but it does not appear to have had anything to do with politics," said Berlin police spokesman Bernhard Schodrowski told the Reuters news agency. "That's all under investigation and he is still in detention being questioned."
The Siegessäule, as the Victory Column is known, has been blocked off on all sides in preparation for Thursday's highly-anticipated speech.
Police have planned for at least 700 officers to be present at the event, where they expect tens of thousands of spectators. The city has been put on the second-highest security threat warning. The US secret service will be in charge of Obama's security while he visits the city on his international campaign tour, which has already made stops in Iraq and Afghanistan.