Nathell was a narrow second after the winner Fernando Pimenta, Portugal, at the finish, but secured the silver a hundredth of a second before the third-placed Bálint Kopasz, Hungary.
Nathell reached the Olympic Games final on the distance last summer, but then had to settle for a seventh place.
In the European Championship final in the Czech Republic, the 30-year-old had the Olympic Games gold medalist and home hope Josef Dostál (fourth) behind him at the finish.
