Pechyonkina clocked 52.34 seconds in the final to break the 52.61s mark set by American Kim Batten when she won the gold medal at the 1995 World Championships in Gothenburg, Sweden.
Pechyonkina, who finished second at the 2001 World Championships in Edmonton, Canada, under her maiden name Nosova behind Morocco's Nezha Bidouane, was herself surprised by her time.
"I was hoping to run fast, but I didn't expect a world record, that's for sure," said the 25-year-old, who ran 53.52s -- the world's best time this year till today -- on Thursday.
Russia's head athletics coach Valery Kulichenko was also in a state of shock. "We all knew she was well prepared, but nobody really expected her to run that fast here," he told Reuters.
"I was hoping she would break the record in Paris, but of course, I will take it anytime. I just hope she will be able to keep her form through the World Championships."
The national championships, being held in the industrial city of Tula some 200 kilometres south of Moscow, serve as qualifiers for the Paris World Championships later this month.