Konstantin Bazelyuk netted twice for CSKA with Syvatosvlav Georgievsky adding a third as the Russian side moved into the last eight of the tournament which pits the best youth sides in Europe against each other.
The Russians started the game well, looking controlled and assured when in possession and pressing high up the field without it.
The impressive Bazelyuk opened the scoring on 11 minutes for the NextGen debutants with a fine finish and grabbed the second 10 minutes later with a clever touch past keeper Eric Verstappen.
PSV had chances of their own near the end of the first half through Rai Vloet but he was unable to convert them and the score remained 2-0 at the break.
The second half continued very much like the first, with CSKA pushing hard for a game-winning third goal.
That crucial goal came in the 68th minute when substitute Georgievsky found the corner of the net with a scrappy finish inside the six-yard box to send his side through to the quarter-finals.
CSKA Moscow will now travel to either Internazionale or Arsenal, who play each other next week.
Tottenham, Sporting Lisbon and Aston Villa had already sealed their passage to the quarters.
Last 16 fixtures / results:
CSKA MOSCOW 3-0 PSV EINDHOVEN
PARIS ST GERMAIN 1-1 a.e.t. TOTTENHAM HOTSPUR (Spurs win 4-3 on penalties)
SPORTING CP 4-0 LIVERPOOL
BARCELONA 0-2 CHELSEA
AJAX 1-2 ASTON VILLA
INTERNAZIONALE v ARSENAL - 06/03/13
OLYMPIACOS v ANDERLECHT - 28/02/13
JUVENTUS v ROSENBORG - 07/03/13
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