A late goal from Papiss Cisse was enough to edge the Magpies past the 10-man Russians, who had Mehdi Carcela-Gonzalez sent off for two yellow cards.
And Hiddink believes his side were clearly the dominant force at St James' park, but paid the price for not displaying a ruthless streak.
He told reporters after the game: “If we would have had a jury tonight we would have won unanimously. We needed to be more effective. Newcastle proved their effectiveness with their final chance.
“We created three to four open chances in the first half and could have killed the game within 17 minutes. We can blame ourselves. We failed to have a lethal weapon.”And after playing the final 35 minutes of the game with 10 men, the 66-year-old criticised the referee for succumbing to the pressure of the home support.
“We were still organised after that. Of course it is bitter when you lose in the last minute," he added.
“I wanted to sub the player but he got a second yellow before I could do it. I think the referee was influenced by the booing of the crowd. It [the second yellow card] was not a wise decision by Carcela.
“Playing like this gives us confidence for our future in the Russian Premier League.”