The Swiss said he was "moved" by the award and stated he was receiving it on behalf of all members of FIFA.
"But the honour really belongs to Germany," he added.
Merkel used the opportunity to wish Italy and France luck ahead of the final in Berlin on Sunday and to congratulate the German team for reaching the semi-finals.
"The whole country is behind this team," she said.
There have also been calls for German coach Jurgen Klinsmann to receive the award after leading Germany to the semi finals.