Shabayeva, 27, the daughter of immigrants from the Republic of Georgia who moved their family to Brooklyn, impressed the show's judges with an edgy collection of 13 looks shown at New York's Fashion Week earlier this year.
The designer said she was inspired by "what it takes to survive in the city as a woman."
"Your line was sleek, modern, cohesive and it told a story," Heidi Klum, the show's host and one of its judges, told the winner.
Shabayeva was joined by runners-up Carol Hannah Whitfield and Althea Harper in the show's second consecutive all-female finale, the show's first outing on Lifetime network after a successful run on rival Bravo.
The finalists were enshrouded in a veil of anonymity at the Bryant Park fashion shows filmed in February due to legal wrangling when "Project Runway" producer, Weinstein Co., sold the hugely popular show's rights to Lifetime after five seasons on Bravo.
A lawsuit by Bravo owner NBC Universal kept any of the Los Angeles-based season's episodes from being aired. After a settlement in April in which Weinstein agreed to pay NBC Universal for the move, the show finally premiered on Lifetime in August, nearly a year after filming had begun.
Originally the finalists showed their runway collections without showing their faces, because the series had not yet aired and the network wanted to maintain suspense over which contestants had prevailed.
Yet each was somehow shown introducing their runway shows during Thursday night's broadcast and walking the runway to applause.
The judges took issue with lack of color in Shabayeva's nearly all-black collection, which featured oversized shawl collars, hooded sweaters, and highly structured heavy wool and felt, but they praised her reach and sense of showmanship.
The outspoken Shabayeva, a frontrunner who often said during the series that she was not there "to make friends," received a fashion magazine spread, a Paris holiday and $100,000 for her victory, not to mention invaluable industry exposure.
Having noted her traditionally minded father's disapproval of her career choice, the winner said: "I think he finally is going to take me seriously about this whole fashion adventure."
Challenges this season ranged from recutting recent divorcees' wedding gowns to suit their new lives, to red-carpet looks and designs for pop star Christina Aguilera.
Throughout the season, a contestant is typically eliminated at the end of each weekly show. The runway finale is taped, edited and shown on television soon afterward, but the court battle delayed it by well over six months.
