Connecticut will play either third-seeded Los Angeles or No. 4 seed Minnesota on Thursday in another single-elimination round.
Thomas beat the halftime buzzer with a hook shot in the lane to tie it at 41, and Connecticut started the second half on a 13-2 run with six points from Jasmine Thomas. Chicago was outscored 27-11 in the game-changing quarter.
Brionna Jones added 12 points and eight rebounds for Connecticut, which overcome a franchise-worst 0-5 start to the season. The Sun had a 40-21 advantage on the glass.
Allie Quigley scored 19 points on 7-of-9 shooting, Kahleah Copper added 17 points and Gabby Williams had 16 for Chicago. Courtney Vandersloot had 12 points and six assists.
It was a memorable season for Vandersloot, who became the first player in WNBA history to average 10 assists per game after totaling 220 in the shortened 22-game regular season.
Bonner left wide open for deep Sun triple
Briann Januar passes to DeWanna Bonner in transition and she knocks down the 3-pointer from way beyond the arc to extend the Sun's lead.