Gonzalez gave Chile the lead with a 7-6, 7-6 win over Novak before Stepanek defeated Marcelo Rios 6-3, 7-6 to level the tie.
The Chilean pair then overpowered Novak and Stepanek 6-4, 6-2 to win the trophy in Chile’s fourth appearance in the event.
Having dropped only one rubber in their three group matches, Chile made the perfect start.
Gonzalez looked in serious danger of losing his first set of the week when Novak raced to a 4-0 lead in just nine minutes, but a break of serve in the fifth game settled his nerves.
Another break in the seventh game put him back on terms and after holding on to force a tiebreak, which he took 7-4.
Rain forced the players off court for an hour during the second set and when they returned, Novak forged ahead again but when he served for the set at 5-4, Gonzalez showed great resistance and resolve to break back.
Novak saved two match points at 5-6 to force a second tiebreak but Gonzalez clinched victory on his third match point.
After Chile’s win over defending champions Argentina on Friday, Rios had warned that he could struggle against Stepanek, and so it proved as the Czech’s guile took him to the first set in 30 minutes.
Rios, who impressed in his victory over Gaston Gaudio on Friday, broke Stepanek to lead 3-1 in the second set only to hand the break back to the Czech in the very next game.
Results of finals:
Chile beat Czech Republic 2-1 (Chilean names first):
Singles: Fernando Gonzalez beat Jiri Novak 7-6 (7-4), 7-6 (7-5); Marcelo Rios lost to Radek Stepanek 3-6, 6-7 (5-7).
Doubles: Gonzalez/Nicolas Massu beat Novak/Stepanek 6-4, 6-2.—Reuters