The seventh-seeded Cibulkova of Slovakia was making her debut at the WTA Finals this past week. The two players met earlier in the first match of the round-robin stage with Kerber winning 7-6 (5), 2-6, 6-3.
Kerber had won their last five meetings but now their head-to-head stands at 5-5.
"I have no words, coming here for the first time, the biggest tournament of my life. I still don't know how I won, I put the ball over the net and it went in; it's the happiest moment of my life," Cibulkova said in her on-court interview.
Cibulkova dominated from the outset in the 76-minute match.
"Only in the first two match points I was a little bit nervous, I realized what the situation is," Cibulkova said. "But after that I only had one goal and I knew I could do it."
Cibulkova posted 28 winners against Kerber, who had 23 unforced errors.
Kerber ends the year with the most match wins of the season with a 63-18 record. She won her first two Grand Slam titles at the Australian Open and U.S. Open, was a finalist at Wimbledon and took the Olympic silver medal at the Rio Games.
"It was a tough year with a lot of matches, so I give everything on the court today, the rest of the energy I had left," Kerber said. "Of course, when I'm looking back it's one of my best years. I will go home now and just think about the best moments and the positive emotions."
Cibulkova finishes the year with a record of 53-21 and No. 5 ranking.
"This year has been the longest season in my career," Cibulkova said. "I don't complain. I wouldn't change it for anything in the world."