The scores were 6-4, 6-3.
It was the first Estoril final between the top two seeds since the tournament began in 1990. Nalbandian also won it in 2002.
"To return four years after the first triumph and win again is very positive," said Nalbandian, who won $74,300.
It was the third consecutive year that a player from Argentina played for the title. The others were Gaston Gaudio and Juan Ignacio Chela.
In the first all-Chinese final on the WTA Tour, Jie Zheng beat Na Li, 7-6 (7-5), 5-7, for the women's title at Estoril.
Na retired after the second set with a thigh injury.