Serra came back from a 5-2 deficit in the second set to force a tiebreaker. But Soderling, a two-time finalist including last year, needed trainers to attend to his lower back for nearly 10 minutes between sets.
"After a set like that, you don't want to start the next set quickly,'' Serra said. "I had a chance to relax myself, get collected and I played well.''
Serra broke Soderling's serve to take a 4-2 lead, then, broke again to clinch the match as Soderling racked up a double fault and two errors off his usually strong forehand.
"I was trying to hit quickly to his forehand, then set him up for the back,'' Serra said. "This is a very, very good win for me at a place where I played well last year. I am looking forward to the week.''
Earlier, Ernests Gulbis upended 2003 champion Taylor Dent 6-2, 3-6, 6-2 and wild card Marcos Baghdatis defeated Kei Nishikori, 7-5, 6-3.
Fifth-seeded Marina Erakovic and Michaella Krajicek reached the quarterfinals of the women's draw. Erakovic had to rally past 17-year-old Melanie Oudin 4-6, 6-2, 6-3 in their second-round match. Krajicek beat Kristina Barrois 6-3, 3-6, 7-6 (0).
In first-round women's matches, Stephanie Foretz got by Melinda Czink 6-2, 4-6, 6-2; Severine Bremond cruised past Kirsten Flipkens 6-4, 6-0; and Chanelle Scheepers defeated Lucie Hradecka 6-1, 5-7, 7-6 (5).
Ljubicic falls; Cilic, Mathieu win in Zagreb
Ljubicic falls; Cilic, Mathieu win in Zagreb
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