The step was a “deciding contribution to the legitimacy of the democratic election process in Afghanistan,” Merkel said late on Tuesday in Berlin.
The chancellor added that the election commission had “met international standards to the best of my knowledge.”
Merkel encouraged Afghan voters to return to the polls to choose between Karzai and his opponent Abudullah Abdullah, a decision she said would have great meaning for their country.
On Tuesday, the Independent Election Commission (IEC) reported that Karzai had not received an absolute majority in the presidential election due to widespread fraud. Karzai, who maintains that he won the vote, still decided to bow to immense international pressure for the second election.
The runoff is scheduled for November 7.