The Wimbledon champion took command in the last two sets with powerful serving, smashes and aggressive groundstrokes against her Russian opponent.
"I'm so excited," Williams said. "That was a hard-fought match, every point, right down to the end."
Williams won $1.34 million at the event, which for the first time offered the same prize money as the men at the ATP's season-ending Masters Cup.
The first lady of Qatar, a conservative Muslim sheikdom, presented the trophy to Williams, shaking her hand and kissing her on both cheeks. Sheika Mozah bint Nasser al-Missned wore a traditional black head scarf and robe.
"Thanks to your Royal Highness for coming. Wow!" Williams said.
Such a public appearance by a ruler's wife is unusual in the region. Mozah might be one of several wives; many emirs and kings in the Gulf have multiple wives - up to the four permitted by Islam.
Billie Jean King sat with Mozah and other dignitaries during the match and joined Williams on the court for the awards ceremony. The trophy is named for King.
Williams' ranking will improve to No. 6 from No. 8, while the ninth-ranked Zvonareva also will move up two spots. The two were the lowest-ranked players at the event, which featured the top eight players in the world.
"I know I can go higher" in the rankings, said the 28-year-old Williams, a former No. 1 who defeated top-ranked Jelena Jankovic in the semifinals.
Zvonareva became increasingly frustrated and collapsed to the ground in tears when Williams broke her in the final set to go up 3-1. Williams, who lost in their first meeting at the 2003 French Open, now holds a 6-1 record against her.
"She stayed aggressive," said Zvonareva, who last qualified for the championships in 2004. "In the second and third, she was dictating."
Zvonareva surged to a 5-2 lead in the first set, and led 5-3, 40-0. But she was unable to convert four set points in that game, and Williams won it on her second break point.
In the tiebreaker, Zvonareva fell behind 1-5, but rallied to win it when her backhand slice clipped the net cord and dropped over.
Williams dominated the second set, not allowing Zvonareva to win a game.
Zvonareva broke Williams with a drop shot to trail 2-1 in the third set. She held serve at love to come within 4-2, her first hold since the first set. But Williams won the next two games to capture the title.
Williams qualified for the championships for the eighth time since 1998. She had reached the semifinals twice and withdrew five times because of injuries and illness.
"It was missing, this one," Williams said of the WTA Championships title. She has won 39 tour singles titles, including five Wimbledon and two U.S. Open crowns.
Williams' career earnings rose to $21.9 million.
In doubles, Cara Black and Liezel Huber defeated Kveta Peschke and Rennae Stubbs 6-1, 7-5.