Arnaut Danjuma scored a brace and Villarreal then withstood a late charge from hosts Atalanta to win 3-2 and secure the last berth in the round of 16 of the Champions League on Thursday.
The match was postponed by a day owing to heavy snowfall on Wednesday but the Spanish visitors were undeterred and 3-0 up after 51 minutes from Danjuma's double and Etienne Capoue netting in-between.
Atalanta rallied from Ruslan Malinovskyi in the 71st and Duvan Zapata nine minutes later but were unable to complete a full turnaround they would have needed to advance.
Instead, Villarreal join group winners Manchester United in the last 16 while Atalanta move into a play-off against a Europa League runner-up for a place in the last 16 of the second tier event.
The draws for the Champions League last 16 and Europa League play-offs are on Monday.
