The 16-year-old beat training partner Kamila Valieva and Alexandra Trusova as Elizaveta Tuktamysheva finished seventh; Tarasova/Morozov win pairs title.
Despite seemingly struggling for breath after Friday's short program having recently recovered from pneumonia, the 16-year-old landed two quads in a near-flawless free skate to "Morning Passages", "Big Plans" and Beethoven's "Five Secrets".
She scored 183.79 for a winning total of 246.10, just over 10 points clear of training partner Kamila Valieva with Alexandra Trusova almost eight points further back in third.
The 16-year-old's triumph even had her coach, the usually impassive Eteri Tutberidze, in tears.
"I was sure that I wanted to go out and show what I can do." - Anna Shcherbakova to 1RT
Shcherbakova is the first woman since Irina Slutskaya (2000-02) to win three consecutive Russian ladies' singles titles.
It was a day to forget for Elizaveta Tuktamysheva whose trademark triple Axel let her down as she finished down in seventh place, a result which leaves her likely to miss out on the Russian squad for March's World Championships in Stockholm.
The event was missing a number of big names with Alena Kostornaia and Evgenia Medvedeva - who was watching in the crowd - pulling out due to COVID, and PyeongChang 2018 gold medallist Alina Zagitova focusing on her television career for now.
While it was Shcherbakova who took the spoils, all three podium occupants produced free skates of the highest quality.
Having struggled with her quads in recent weeks, Trusova opted to include just two in her free skate - a quad Lutz-triple toe loop combination and a quad Lutz which she just about held onto.
That paid dividends in a clean free skate to the Romeo and Juliet soundtrack with coach Evgeni Plushenko giving a 'thumbs up' having been visibly annoyed at how she was scored in the short program.
She was awarded 170.61 for a formidable total of 246.37 with three skaters to come.
Then came reigning world junior champion Valieva who had arguably her best skate yet to Ravel's 'Bolero'.
The 14-year-old's jumping was as accurate as it has been, opening with a quad toe loop-double toe loop combination followed by another quad toe.
While she is too young for the upcoming World Championships, Valieva showed she will be a serious contender when she steps up to the senior ranks next season.
Her score of 174.02 put her in the lead on 254.01 with only overnight leader Shcherbakova in with a chance of eclipsing that tally.
But the reigning champion rose to the challenge having spoken yesterday of needing to fight her way through her recent illness.
Shcherbakova, the only one of the famed '3A' remaining at the Sambo-70 club with Kostornaia and Trusova moving to join Plushenko, looked like she meant business as she landed her opening quad Lutz.
That was followed by an equally immaculate quad flip which also attracted high execution marks from the judges, and an exceptional display of jumping and artistry resulted in a clear victory for Shcherbakova who is perhaps the only skater certain to represent Russia in March's World Championships.
Daria Usacheva skated last and finished fourth, well clear of Maiia Khromykh, as Tutberidze skaters filled four of the first five places.
Elizaveta Nugumanova was sixth with Tuktamysheva seventh.
Reflecting on recent events, Tutberidze told 1RT, "It was about overcoming this period. Our work has paid off. I am very proud of Anna but I also want to give credit to Kamila. Both girls gathered themselves and did great. It was very much about the sport."
Her choreographer Daniil Gleikhengauz added, "We were prepared for all eventualities and for Anna not being able to compete. But we knew that whatever we told her wouldn't stop her from going out and doing it."
It wasn’t a perfect performance for PyeongChang 2018 team silver medallists Evgenia Tarasova and Vladimir Morozov, but they delivered an inspiring weekend of skating in Chelyabinsk to reclaim the Russian national title in a competitive pairs field.
Skating to “Adagio” in a moving free skate, Tarasova and Morozov continued their momentum from a standout short program only to be felled by a fall on a throw triple Salchow, their final major element of the program.
But they were otherwise outstanding, skating with emotion and connecting their world-class elements with brilliant skating as they scored 147.58 for a winning total of 228.23.
They won the free skate by just 0.07 from Aleksandra Boikova and Dmitrii Kozlovskii, who stayed upright but weren’t perfect themselves in the free, including Boikova saving an early side-by-side triple Salchow and a step out on a throw triple flip in their “The Writing’s on the Wall” James Bond program.
Having been second after the short program, Boikova and Kozlovskii finished just over three points behind with 224.99.
Daria Pavliuchenko and Denis Khodykin were third in a tight competition, almost the same margin behind the runners-up with 221.39.
The Russian pairs teams now look to Worlds – though the final selection will be announced at a later date – where they will look to topple China's reigning champions Sui Wenjing and Han Cong.