Older sister Venus Williams alsa advanced by ousting Shahar Peer of Israel 6-3, 6-4. Both sisters are back from knee injuries, and could meet in the semifinals after being placed in the same half of the draw.
Serena had been off the tour since she won the singles and doubles at the Australian Open, and she was entered in Rome thanks to a wild card.
Against the 49th-ranked Petkovic her game was erratic at times. She closed the match with almost as many winners as unforced errors, 25 to 21.
Serena got off to a good start, winning the first set with a five-game streak. But she quickly fell 4-1 behind in the second, came back to 4-3 but conceded another, decisive break to Petkovic. In the third set, she picked up her game and played aggressively.
The fourth-seeded Venus, who had been sidelined with a knee problem since losing the Key Biscayne final, broke once in the first set and dropped just four points on her serve. Both players then lost serve early in the second, and Venus had to save two break points at 4-4 before getting the decisive break in the next game with a forehand winner.
She saved another break point when serving for the win before converting her second match point.
Also, Nadia Petrova of Russia won 6-0, 3-6, 6-2 against Alexandra Dulgheru of Romania, who knocked out defending champion Dinara Safina on Tuesday.
In other third-round matches at the clay-court Foro Italico, fourth-seeded Venus Williams took on Shahar Peer of Israel and two-time former champion Jelena Jankovic was up against Yanina Wickmayer of Belgium.