The seventh-seeded Cibulkova, making her debut at the WTA Finals this week, picked the right match to win against Kerber during the week. The two met in the first match of the round-robin stage on Sunday with Kerber prevailing 7-6 (5), 2-6, 6-3.
"Coming here for the first time and winning the biggest title of my life, I have no words," Cibulkova said. "Today you can see I got really lucky in the end."
Kerber had won their last five meetings, but now their head-to-head stands at 5-5.
The only time Cibulkova looked nervous in the 76-minute match was when she was serving for it at 6-3, 5-4. She missed on three match points and saved two break points before a forehand clipped the top of the net and just dribbled over to give her the victory.
"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."
From the minute Cibulkova hit the first ball of the match she was on fire, taking Kerber out of her game, belting winners at will, and in complete command of the outing.
In contrast, Kerber never showed the skills that led her to the No. 1 ranking. She appeared frustrated and unable to contend with the variety of Cibulkova's shot-making.
"In the first match I played against Angelique (this week), that match gave me confidence that I could beat her," Cibulkova said. "With this thought I was going into the final and I was feeling it from the first point to the last point. I didn't let her into the match today with my being aggressive."
Cibulkova posted 28 winners to only 14 for Kerber, and had only 14 unforced errors to 23 for Kerber.
Cibulkova, who will end the year ranked No. 5, is the second consecutive player to win the WTA Finals after going 1-2 in the round-robin stage of the competition. Kerber went 3-0 in the round-robin.
Last year, Agnieszka Radwanska won the trophy after posting the same record in the round-robin.
Cibulkova closes out the year with a record of 53-21, which is the most tour-level matches she's won in a season in her career.
"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."
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 US Open, was a finalist at Wimbledon, and captured the Olympic silver medal, which ensured she took over the No. 1 ranking last month.
"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 home now and just think about the best moments and the positive emotions," she added.