Nadal broke Souza's service late in each set to win in 1 hour, 18 minutes at the indoor clay-court tournament in South America's biggest city.
The victory over the 140th-ranked Brazilian came a day after Nadal withdrew from the doubles tournament to preserve the sore knee that sidelined for seven months. The 11-time Grand Slam winner, the tournament champion in 2005, had a bye in the first round.
"Today I felt good," Nadal said. "It's not perfect yet, I don't know when I'll be at 100 percent. It was acceptable. I'm confident that as the days and weeks go by I'll recover what's still missing."
Nadal will face Argentina's Carlos Berlocq, a 7-6 (7), 6-4 winner over eighth-seeded Albert Ramos of Spain.
Nadal lost the singles and doubles final last week at the VTR Open in Vina del Mar in Chile.
Earlier in the day, defending champion Nicolas Almagro of Spain beat Chilean qualifier Paul Capdeville 6-4, 6-7 (3), 6-2.
The 11th-ranked Almagro won the last four games to stay on track for his third straight title in Sao Paulo — and fourth overall. Almagro won the tournament for the first time in 2008 and then in 2011-12.
"Hopefully, I'm on my way to winning another title here," said Almagro, who had 18 aces in a match that lasted nearly two hours. "I've been successful in Brazil so far and I hope it continues like this for a long time."
The second-seeded Spaniard will face David Nalbandian, a 6-4, 6-2 winner over Guido Pella in an all-Argentine match.
The Brazil Open is Almagro's first tournament since his five-set loss to compatriot David Ferrer in the Australian Open quarterfinals in January.
Third-seeded Juan Monaco lost an opening-round match for the third time this season, falling to Simone Bolelli of Italy 7-5, 6-2. The 15th-ranked Argentine had his service broken four times in the second-round loss at the Ibirapuera arena.
Monaco, who had a bye in the first round, lost his opening match at the Australian Open and last week in Chile.
The 80th-ranked Bolelli needed 1 hour, 16 minutes to beat Monaco and advance to the quarterfinals in Brazil. Bolelli will face Albert Montanes, who beat seventh-seeded Pablo Andujar, also of Spain, 7-5, 6-2.
Italy's Filippo Volandri beat fifth-seeded Thomaz Bellucci, Brazil's top ranked player, 6-3, 6-2.
Nadal and Almagro have been some of the many players complaining of bad court conditions in Sao Paulo, arguing the surface is too slippery and dangerous to players' health.
"The court is not good, but it's not good to all players," Almagro said. "You have to try to forget about that and play the best you can. But it's clear that for the future this is an aspect that they (organizers) will have to improve."
The tournament was played in the northeast coastal city of Costa do Sauipe from 2001-2011, moving to Sao Paulo for the first time last year.