Samara, who have dropped to 12th following a seven-game winless streak, said on their website they had accepted Kobelev's resignation.
The 44-year-old former Russia midfielder had coached Samara since July 2011, saving the club from relegation that year.
He also coached Dynamo Moscow from 2006 to 2010 before being sacked following a string of poor results.
Fellow strugglers Alania Vladikavkaz sacked Vladimir Gazzayev, who at 32 was the youngest coach in the Russian Premier League, on Wednesday.
- Sports & Recreation
- Vladimir Gazzayev