Safarova sealed the matched in the best-of-five series with a forehand winner on her second match point before an ecstatic sell-out home crowd on a hard court in the O2 Arena.
The Czechs are the third country in a row to successfully defend the Fed Cup title. Russia won in 2007-08 and Italy 2009-10.
The Czechs took a 2-0 lead after the opening singles on Saturday but Ana Ivanovic's victory earlier Sunday halved that advantage by beating Petra Kvitova 6-3, 7-5.
It was the first loss for Kvitova after 11 straight Fed Cup singles wins.