Malki opened the scoring after 10 minutes with a deflected header off the shoulder of Simon Poulsen, and 12 minutes before the interval Junker (pictured) finished a cross from Mitchel Donald to seal victory.
PSV Eindhoven had taken first place in the league with a 3-1 win over Vitesse Arnhem on Friday, and Alkmaar's defeat meant they failed to reclaim the top spot they had held since September 25.
PSV have 41 points from 19 matches, two points ahead of Alkmaar in second.
Heerenveen drew level on points with Ajax with a 2-0 win over Utrecht on Saturday. Both goals came in the first 15 minutes, from Bas Dost and Jeffrey Gouweleeuw.
In other games on Saturday, NAC Breda and Graafschap Doetinchem shared the points in a 1-1 draw, while struggling Excelsior Rotterdam suffered a 3-0 defeat against 10-men Heracles Almelo.
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