The Russian team also piled on the agony for the winless Dutchmen, who dropped their fifth game in the competition.
The home side, which won the first encounter between the two sides 78-69 in the Netherlands back on December 1, will next week travel to Italy to face Scavolini Pesaro looking to win for the sixth time in a row in Europe.
Krasnye Krylia had already booked their place in the Last 16 while Amsterdam had no chance of advancing.
The Dutch outfit did lead 20-18 midway through the second quarter but Evgeny Voronov dunked and Andrey Ivanov buried a three-pointer to put Krasnye Krylia in front to stay.
In Tuesday's rout, Ralph Biggs played big for the winners with a game-high 14 points.
He buried four of five shots from long range.
Andrey Ivanov finished with 12 points, Evgeny Voronov 11 and Luis Flores nine.
Sergei Mokin's men out-rebounded Amsterdam 46-23.