The two players combined to score 51 of their team's points, with McCoughtry pouring in a season-high 28 while also bringing down 15 rebounds.
Kosice, despite the Christmas-break departure of Linda Fröhlich to Municipal Targoviste and injury problems, looked as good as ever in clinching second spot in the group, a finish that is likely to earn them a much more favorable tie in the Eighth-Finals Play-offs.
Dupree finished with 23 points and 11 rebounds while teammate Miljana Musovic scored 12 points, handed out six assists and corralled four rebounds.
Prague forced their opponents to turn the ball over 20 times, yet they didn't compete with them on the boards as Kosice out-rebounded the home side 46-32.
The hosts had a good start, opening up an early 15-7 lead with Sonja Kireta scoring six points.
Kosice fought hard and didn't allow Prague to build on the advantage.
Instead, the Slovakians began to make their move two minutes into the second quarter when they trailed 27-26.
Dupree and McCoughtry scored all of the points in a 14-0 spurt that put the visitors in front for good.
A Musovic three-pointer at the buzzer from half-court gave Kosice a 51-37 lead at the break and they kept the pressure on in the third, taking a 65-55 lead into the final quarter.
Kireta battled, with two free-throws by the Croatian center reducing the deficit to 67-59.
A Katerina Elhotova lay-up for Prague and five straight points by teammate Evina Maltsi, including a shot from long range, cut the deficit to 69-66.
Not long after and Dupree and McCoughtry caught fire again, scoring all of the points in a 13-0 run that gave Kosice an 87-71 lead and effectively put the result beyond doubt.
For Prague, Kireta finished with the 21 points while Lindsay Whalen contributed 15 and Maltsi 12.