The Dutch global placed Atalanta in advance inner 3 minutes and Etienne Capoue doubled the lead quickly before 1/2-time on some other cold nighttime in Bergamo.
Danjuma scored again early within the 2nd half of but Villarreal were compelled to preserve on as Atalanta spoke back with goals from Ruslan Malinovskyi and Duvan Zapata whilst hitting the woodwork 3 times.
Villarreal finished as runners-up to Group F winners Manchester United, with Atalanta going into the Europa League knockout-round play-offs in February.
Quarter-finalists seasons ago, Atalanta needed a win to climb above Villarreal into 2d area inside the institution but made a disastrous begin to a game driven again from Wednesday after a cold snap swept throughout northern Italy.
Merih Demiral lost ownership and Dani Parejo sent Danjuma clear of the Atalanta defence to fit among the legs of goalkeeper Juan Musso.
Atalanta captain Rafael Toloi headed over from a free-kick and Remo Freuler drew a flying keep from Geronimo Rulli, but Villarreal made it 2-0 as Capoue controlled inside the place and drilled home.
Gerard Moreno installation Danjuma to seize Villarreal's 0.33 on fifty one mins, apparently finishing any hopes for Atalanta.
Malinovskyi clipped the bar just before the hour with a loose-kick and Zapata shaved the outdoor of the publish.
The hosts in the end pulled one lower back thru Malinovskyi's deflected drive with 20 mins to play and Zapata dinked over the advancing Rulli to provide Atalanta desire.
