Pavlyuchenkova, who won her first two tournament titles earlier this season, served for the first set at 6-5, only to be broken and then defeated in the tiebreaker.
Her Slovak opponent called for a trainer to have her back treated as she trailed 2-1 in the second set and Pavlyuchenkova, who reached a career-high 19th in the rankings on Oct. 4, went on to level the match. However, she failed to win a single service game in the final set.
“It was absolutely my fault,” Pavlyuchenkova said. “I was disappointed after the first set but it looks like I relaxed after a relatively easy second set. I have no explanations. I beat her in straight sets in Tokyo a couple of weeks ago.” Pavlyuchenkova failed to make it to the second round at her hometown event for the fourth time.
Elsewehere, eighth-seeded Maria Jose Martinez Sanchez of Spain advanced to the second round by beating Russian wild card entrant Alla Kudryavtseva 6-1, 5-7, 6-1.
The 28th-ranked doubles specialist Martinez Sanchez, who is looking for her fourth singles title, easily won the first set. Kudryavtseva, who won her first WTA Tour title in Tashkent in September, leveled the match at 1-1, but could not keep the pace and was broken twice in the decisive set to lose the match.
In the other completed match, Kateryna Bondarenko of the Ukraine defeated Petra Kvitova of Czech Republic in three sets.
In men's action, seventh-seeded Sergiy Stakhovsky of Ukraine rallied in the third set to beat Michael Russell of the United States, 6-4, 3-6, 7-5.
Three-time champion Nikolay Davydenko tops the men's draw of the 21st edition of the event. Jelena Jankovic, who won in 2008, leads the women's draw.
Jankovic is among the eight players who have qualified for next week's season-ending WTA Tour championships in Doha.
Victoria Azarenka of Belarus, seeded second at the Kremlin Cup, and third-seeded Li Na of China will go to Doha as substitutes. Li is just five points ahead of Azarenka in the championship rankings and whoever fares better in Moscow may be required to replace Serena Williams in Doha.
Williams, who had been sidelined since July after cutting her foot on broken glass, was planning a comeback in Linz, Austria, last week, but withdrew after restraining her injured foot. She has announced that she might be out for the rest of the season, but is yet to confirm that.
“That's why I have chosen Moscow,” said Li, who entered the event on a wild card. “This is my last chance to be at Doha and I do not want to lose this chance.”
