Petrova, ranked No. 10 in the world, won nine of the last 11 games to beat Keys, who was playing in her first WTA Tour event in the season-opening clay-court tournament.
"At the beginning of the match I didn't know what to expect,'' the Russian said. "She caught me by surprise.''
The Russian is playing in only her second tournament since suffering a "stress reaction'' to her right foot in December. She said the foot is aching "from time to time'' but isn't hampering her on court.
The match was tied 3-3 in the first set before Petrova won three straight games.
"I had to make some adjustments,'' she said. "I was trying to go for too many winners early, trying to blow her away and just had to slow down.''
Despite the loss, Keys was pleased with her play.
"When I hit a good shot she hit a good shot back,'' she said. "I feel pretty good about going 3 and 2 with a top 10 player.''
Petrova advanced to a quarterfinal match against seventh-seeded Alona Bondarenko of Ukraine. They played once, two years ago, in a match Petrova won.
Bondarenko won 11 of the last 15 games to beat her younger sister, Kateryna, 4-6, 6-4, 6-3 earlier in the day.
The 24-year-old Alona, two years older, fell behind 3-1 in the second set. She rallied to break serve throughout the set, which included a 13-deuce and nine-deuce game and lasted 54 minutes.
"We have different styles, but we know each other well,'' Alona said. "I have to play the long points and she doesn't.''
The Ukrainians traded games early in the third set and were tied at 3-3 before Alona broke twice and won the final three games.
Alona's win tied the sisters' series at 3-3. They last met in 2006.
In other matches, third-seeded Dominka Cibulkova of Slovakia defeated Anastasia Rodionova of Russia 6-1, 6-3. Cibulkova lost in the final last year to Maria Sharapova.
"I was pretty confident from the baseline,'' she said. "I'm playing pretty solid.''
In the quarterfinals, Cibulkova will meet Elena Vesnina of Russia, who defeated Patricia Mayr of Austria 1-6, 6-3, 6-2.
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