كتب : Mohamed Sabe
The win handed Real Madrid their first three points in the group to come in second place, three points behind leaders Lyon who crushed Steaua Bucharest 3-0.
Van Nistelrooy opened Real's account when he notched home from point blank ranged after Dynamo keeper Olexander Shovkovsky fumbled a Roberto Carlos cross.
Raul added the second in the 27th minute when he connected with an inch-perfect Jose Antonio Reyes cross to head home.
Reyes turned scorer on the stroke of half-time after collecting a Mahamadou Diarra pass.
Dynamo pulled one back through Artem Milevsky two minutes after re-start, but the Ukrainian side soon received another blow.
Raul compounded Dynamo's misery when he pounced on a mis-pass from Goran Gavrancic and rounded the hapless Shovkovsky to tuck home the fourth.
Dynamo where reduced to ten men when Shovkovsky towed down Van Nistelrooy in the area.
The Dutchman stepped up to successfully convert the spot-kick past reserve goalkeeper Olexander Rybka.
Dynamo lie in last spot in Group E with no points.
Elsewhere, Lyon grabbed the group summit after a 3-0 away win over Steaua Bucharest.
Brazilian striker Fred put Lyon ahead when he made the best of a blunder from Steaua keeper Carlos Fernandez.
Fernandez surprisingly dropped an easy Juninho free-kick only for the Brazilian to notch home the opener.
Juninho continued his good showing and dished out two assists to Tiago and Karim Benzema in the second-half.