Williams had taken up a wildcard to play in the tournament following an early exit in Rome, where she was beaten by Nadia Podoroska in her opening contest in the clay-court swing.
Her campaign in Parma got off to a better start on Monday, a 6-3 6-2 result against WTA Tour debutant Lisa Pigato bringing a first triumph since losing in the semi-finals of the Australian Open in February.
Serena sails through but Venus falls at the first hurdle in Parma
However, the 23-time grand slam champion was unable to repel a determined Siniakova as she slipped out at the last-16 stage.
“It was a fantastic match and I played so well, I’m so happy that I could finish like that,” Siniakova said after recording a 7-6 (7-4) 6-2 result.
“It was a pleasure to share the court with her.
“Now I will have the pressure because I defeated a great player, but I will enjoy it. I’m happy that I can continue and I will try to play my best in the next match.”
Having failed to convert a set point opportunity, Williams hit back after losing serve with a break of her own to force a tie-break in the opener.
But Siniakova forced her way into a 5-3 lead before sealing it with a service winner, then quickly seized control of proceedings in a second set which was far less competitive.
Third seed Coco Gauff came through two tie-breaks to see off Kaia Kanepi, the American teenager having let slip a 5-1 lead in the second set before eventually sealing a 7-6 (8-6) 7-6 (9-7) win.
Petra Martic had no such issues in her opening contest against Varvara Gracheva, the second seed easing through 6-4 6-2 after one hour and 21 minutes on court.
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