The 21-year-old, skating to "Blues for Klook" by Eddy Louiss, hit a quadruple Lutz-triple toeloop combination as he claimed 92.81 points to finish two clear of compatriot Dmitri Aliev, who scored 90.64.
To the delight of the home fans, Makar Ignatov completed an all-Russian podium with a score of 87.54 as the 19-year-old shone on his Grand Prix debut. Less than one point separated third from sixth place as Japanese Olympic silver medalist Shoma Uno narrowly missed out on the top three with 87.29 points.
Deniss Vasiljevs, with 87.08 points, followed by Canada's Nam Nguyen, 87.01, rounded out the top six.
"I felt a lot of warmth, I enjoyed skating here," Samarin said.
"I made some mistakes, but the competition is not over yet and I hope to speak more tomorrow.
"You can always make something even more complicated. I have to deal with the combinations I have. At the moment we have a plan and we are going according with it."