Defending champions Spain had sealed their fourth Davis Cup title on Saturday when the doubles pair of Fernando Verdasco and Feliciano Lopez demolished their Czech opponents to give the hosts an unassailable 3-0 lead.
And world number two Nadal and Ferrer completed the job on Sunday by beating Jan Hajek and Lukas Dlouhy respectively for a final 5-0 scoreline for the hosts.
Nadal downed Jan Hajek 6-3, 6-4 while Ferrer cruised to a 6-4, 6-2 victory over Dlouhy.
Spain becomes the first country since Sweden in 1998 to retain the Davis Cup, after triumphing last year in Argentina.
"It was an incredible moment to return as captain after winning here nine years ago," said Spanish team captain Albert Costa, who as a player helped Spain to its first ever Davis Cup title in 2000, beating Australia at the same Palau Sant Jordi Arena in Barcelona.
Spain won again in 2004, defeating the USA.
On Saturday, Verdasco and Lopez overwhelmed an exhausted Stepanek and Tomas Berdych - who had lost both Friday's opening singles - 7-6 (9/7), 7-5, 6-2, in what was the Czech pair's first ever Davis Cup defeat in six matches.
In Friday's opening singles, Nadal, who had limped out of last week's ATP World Tour finals in London without a single win, cruised past Berdych 7-5, 6-0, 6-2.
Then Ferrer, ranked 18, came back from two sets down to beat Stepanek 1-6, 2-6, 6-4, 6-4, 8-6 in an epic match that lasted four hours and 17 minutes.
The Czechs won their only Davis Cup title as Czechoslovakia with Ivan Lendl in their squad in 1980.