Matteo Boniciolli's Italians, who needed to win to guarantee a place in the Quarter-Finals, prevailed 69-57.
The result knocked EWE Baskets Oldenburg out of contention for a last-eight place.
EWE Baskets had needed to win at Galatasaray on Tuesday and for Virtus, whom they beat twice, to lose in order to advance.
Reshawn Terry had 16 points for Virtus, with Finland international Petteri Koponen and playmaker Earl Boykins contributing 15 apiece.
Kyiv are still in the last eight.
They won their fourth game in the group last week to seal their progression but ended up second in the pool after losing both of their games to Virtus.
Kyiv only trailed 49-43 after Manuchar Markoishvili made a lay-up for the first two points of the fourth quarter.
Ntousan Tsalikis-Vouktsevits replied with a three-ball to settle the Virtus nerves.
After Oleg Saltovets split a pair of free throws for Kyiv, the Italians answered with a 9-0 run.
Six of the points were scored by Terry.
He made a jump shot, then a lay-up and after Boykins sank a three, Terry dunked.
The lead ballooned to 67-47 on a Keith Langford three-ball just 2:39 from the end before Boniciolli's men finished with a 12-point triumph.
Artur Drozdov led all scorers with 20 points for Kyiv.