Thomas had 23 points off the bench and the Suns defeated the San Antonio Spurs 94-89 on Friday night.
After the Suns came close many times throughout the game to take a lead over the defending champs, Thomas blew past Boris Diaw in the open floor to finally put the hosts in front 88-87 with 3:34 left.
San Antonio trailed 92-89 with 6.5 seconds remaining following a timeout, but Diaw was whistled for a five-second violation just before he signaled for a 20-second timeout. Eric Bledsoe sunk two game-clinching free throws at the other end.
Markieff Morris posted 20 points and 11 rebounds, Eric Bledsoe tallied 12 points and nine boards and Alex Len provided his first career double-double, 10 points and 11 rebounds, off the pine for Phoenix, which beat the Los Angeles Lakers in its season opener Wednesday.
"The way he was playing with his length had a real effect on the game," Suns head coach Jeff Hornacek said of Len.
Tony Parker supplied 19 points and six assists, while Tim Duncan added 16 points and nine rebounds for the Spurs, who edged Dallas in their first game of the year on Tuesday.
Parker and Marco Belinelli sandwiched 3-pointers around a Gerald Green triple to stake the Spurs to a 77-70 cushion early in the fourth before three consecutive Thomas buckets trimmed the gap to 77-76.
San Antonio, though, responded with an 8-1 spurt, with a Cory Joseph turnaround jumper providing it an 84-78 spread with 6:53 to play.
Phoenix answered back with a 12-3 surge and Hornacek used a three point guard lineup in the final 4:35.
After Thomas' layup, Morris sunk two free throws and then put down a dunk off a Len interior pass to make it 92-87 in favor of Phoenix with 1:09 left on the clock.
Manu Ginobili was fouled on a three and made 2-of-3 foul shots at the other end. Bledsoe was off on a jumper, Len backtapped the ball back to Thomas to retain possession, but Thomas misfired to give San Antonio possession with 16.9 ticks left.
Earlier, a 15-3 Spurs first-quarter swing gave them an early 24-9 margin and they led 24-11 after the frame.
The Suns began the second with a 13-2 run and later tied the game at 30-30 midway through the stanza after Len threw down an alley-oop pass from Bledsoe.
San Antonio responded by putting in eight straight points and took a 45-36 lead into the break.
The Spurs took a 71-67 edge into the fourth.
Thomas became the fourth Sun, joining Tom Chambers, Tom Gugliotta and A.C. Green, to scored at least 23 points in his first two games with the team ... Phoenix shot just 2-of-18 (11.1 percent) from beyond the arc, but made 22-of-26 (84.6 percent) from the foul line.