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Second-seed Naomi Osaka of Japan also fell at the first hurdle in Rome with defending champion Simona Halep of Romania, the third seed, retiring with a calf injury.
But world number one Ashleigh Barty got off to a winning start, the Australian advancing to the third round in the warm-up tournament before the French Open starts on May 30.
Williams, 39, lost 7-6 (8/6), 7-5 on her return after nearly three months away to Argentina’s Nadia Podoroska, a player 15 years her junior, who was a surprise semi-finalist at last year’s Roland Garros.
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“It was definitely kind of good to go the distance and to try to be out there, but clearly I can do legions better.
“Maybe I do need a few more matches, so I’m going to try to figure that out with my coach and my team and see what we would like to do.”
Williams, a four-time Rome winner and 23-time Grand Slam champion, had not played since her semi-final defeat to Osaka in the Australian Open this year.
And the eighth seed found it tough going, losing in just under two hours to the 44th-ranked Argentine.
“Overall, it was good for me to play such a clay court player on clay today, but it’s a little frustrating,” she conceded.
“Yeah, just filling out the game, finding the rhythm. Even sliding and confidence with that, with movement, and just not wanting to break my ankle when I moved.
“That’s always like a little struggle in the first two matches, and then I’m raring to go.”
The early exit is a blow before the French Open in Paris where the American continues her bid to equal Australia’s Margaret Court’s record of 24 Grand Slam trophies.
Despite a battling performance Williams could not wear down the 24-year-old who broke twice in the first set.
Podoroska forced a tie-break with an ace and squandered three set points before sealing the set.
In the second, Williams was trailing 5-2 but held and broke the Argentine to love while she served for the match to level at 5-5.
Podoroska held her nerve to earn three match points to secure just her third career win over a top-10 player, all in the last eight months.
“It’s a special win, she’s a great athlete, she’s done so many things for our sport,” said Podoroska who next meets Croatia’s Petra Martic.
“It’s history most of all.”
For Williams it was her 149th defeat, with 851 wins over the course of a WTA career spanning 1000 matches.
Days after her shock defeat in the Madrid final, Barty advanced to the third round with a 6-4, 6-1 win over Kazakh Yaroslava Shvedova.
Barty overcame an early break of serve to see off Shvedova, a three-time Grand Slam quarter-finalist making her way back after giving birth to twins.
She next meets 28th-ranked Russian Veronika Kudermetova as she bids for a first Rome quarter-final on her third appearance.
Osaka slumped to a 7-6 (7/2), 6-2 loss to 31st-ranked American Jessica Pegula.
The reigning US and Australian Open champion from Japan has seven career hard-court titles, but has never managed to lift a clay-court trophy.
She was playing just her third tournament since winning the Australian Open in February and also exited in the second round in Madrid earlier this month.
World number three Halep, the 2018 French Open champion, limped off in tears with a left calf issue while leading Germany’s Angelique Kerber 6-1, 3-3 in their second-round tie.
“I’m so disappointed to end my tournament in Rome like this…but I will do everything I can to take care of the injury and be back as soon as possible,” she posted on Twitter.
Former Rome champion Karolina Pliskova, seeded ninth, also advanced along with fifth seed Elina Svitolina of Ukraine.