The Belgium international scored 19 points and grabbed 14 rebounds as the Russian club won 80-72 to improve to 6-4 in Group B and remain in the race for second place.
Becky Hammon contributed 15 points for CSKA, and both Katie Douglas and Edwige Lawson-Wade scored 13 apiece.
Umana Reyer lost for the third straight game in Europe although at 7-0 they had already sewn up first place.
There was no doubting their desire to win in Russia.
Jenifer Nadalin's jump shot at the start of the fourth quarter gave the Italian club a 65-58 lead and CSKA looked to be in trouble.
A pivotal sequence followed, though, as Douglas was fouled while attempting a three-ball and made all the free throws to close the gap to 65-61 with 9:12 remaining.
Following a Nadalin miss, Ilona Korstin scored on a lay-up to cut the deficit to 65-63.
Wauters then added a lay-up before Hammon's second three-pointer finished the 10-0 run for a 65-68 lead.
Umana Reyer went back in front one last time at 71-70 after a Mery Andrade jumper, but Douglas answered for CSKA with a jump shot and then split one of two at the line the next trip down the floor for a 73-71 advantage.
Umana Reyer could have tied the game at the line with 3:40 to go but Giorgia Sottana made just one of two.
Wauters, McCarville and Hammon with her third three-pointer finished off the scoring for an eight-point triumph.
Italy international Simona Ballardini led Umana Reyer with 16 points and Andrade scored 15.
Massimo Riga, head coach Umana Reyer
"We would have liked to win but we didn't do everything for that; still we are satisfied with the overall result because we finished in the first place in the group. We have a very difficult schedule of practices and games; that is why we were quite tired; and on Friday we'll have to play very important game in our national championship, so may be this is the reason why everything wasn't so good today."
Gundars Vetra, head coach CSKA Moscow:
"It is great to end the [regular] season with a victory, and moreover in over the team who finish first in our EuroLeague group. Umana Reyer play good basketball and it is very difficult to [play] against them. At the beginning they scored a lot of easy shots but in the third quarter we cancelled taht and were more careful in defense while we found a way how to play in the offence."