Several internet sites reported that Saturday's game in Krasnodar was fixed after Samara, fighting to avoid relegation, beat the home team 3-0. Krasnodar are in eighth place and are assured of staying in the top flight with just six games left.
In a strongly-worded joint statement, issued by both clubs on Monday, they denied any wrongdoing.
"We believe this is a pure smear campaign, not only against the two clubs but the entire Russian football," the clubs said on their respective websites.
"Such allegations are outrageous and insulting," Samara boss Denis Maslov was quoted as saying by local media on Monday.
"What do you think we could offer Sergei Galitsky so he would agree to give us a win?" he asked in reference to Krasnodar's billionaire owner.
In the past, Galitsky has questioned his players' commitment on the pitch, even suggesting they take a lie detector test.
The Russian Premier League also issued its own statement later on Monday.
"Lately, we have seen an increase of unfounded allegations in the media. Unfortunately, often they are initiated by certain members of our football family," the league said on its website.
"We ask all our members to respect each other. At the same time refrain from making rush conclusions which would harm the reputation of our clubs, the Russian FA and the Premier League."
Last month, the Russian parliament gave preliminary approval to legislation designed to toughen punishment for match-fixing that could send offenders to jail for up to seven years.
Experts say that match-fixing and corruption are rife in Russian soccer as the country prepares to host several major international events including the 2018 World Cup.
However, rarely has anyone been convicted or brought to trial and only one team, second division Iriston Vladikavkaz, have been found guilty of attempted match-fixing.
They were thrown out of the league in 1997 but later reinstated in a lower division.
FIFPro, the global union for professional players, published a survey of nearly 3,400 players from eastern Europe this year that said match-fixing in Russia was as high as 43.5 percent.