Nadal's victory comes four weeks after he lost the Australian Open, beaten in that final by underdog Stanislas Wawrinka after tweaking his back while warming up.
Nadal, who had to fend off two match points in the semifinal against Pablo Andujar, looked more comfortable in the final and improved his record on clay to 298-21, the best in the Open Era.
Dolgopolov has lost all five matches against Nadal.
On the women's side, Kurumi Nara of Japan won her first WTA singles title, defeating top-seeded Klara Zakopalova of the Czech Republic 6-1, 4-6, 6-1.
The 22-year-old Nara was seeded fifth in the tournament and is Japan's top-ranked woman at No. 62. She prefers to play on hard courts but has adapted to the heat and clay in Rio.
"I love Rio," Nara said, cracking a huge smile. "I can't believe I won the tournament, but I am very happy."
The victory is likely to push Nara into the top 50 when the WTA publishes its rankings on Monday.
"I don't want to think too much about being No. 1 in Japan," Nara said. "I just want to focus on my game -- every game."
Nara said she thrived on the hot, humid weather in Rio and said Japanese players are getting better on clay because a new clay-court facility has been built in the country.
Maria Bueno, Brazil's greatest female player who won seven Grand Slam singles titles -- her last in the US Open in 1966 -- helped hand the winning trophy to Nara.
Zakopalova won two WTA titles 10 years ago, but has now lost 12 consecutive singles finals. In parts of the match she seemed unwell, probably bothered by the 32 Celsius (90 Fahrenheit) heat and intense humidity.
"I have an asthma problem so I couldn't breathe," Zakopalova said. "But it's not an excuse. Well done to Kurumi. She deserved it. She played really well."