The 66-year-old former head of the International Monetary Fund had the backing of Chancellor Angela Merkel's conservatives and saw off a challenge by left-wing academic Gesine Schwan.
After his re-election, Köhler said he was confident that Germany would face the economic crisis with courage and emerge stronger after one of its worst financial slumps. "This country is strong," the president said. "We have a lot of work ahead of us but we'll manage to do it."
A failure to get Köhler re-elected would have been a blow to Merkel, just four months before she herself runs for a second term in general elections on September 27.
Köhler was elected by 1,223 MPs and public figures in Berlin and won the 613 votes needed in the first round of voting on Saturday.
Germany's president has few formal powers, although he or she can dissolve parliament and veto laws on constitutional grounds. The president's main job is to represent the country and articulate its values and challenges.