The Swiss world number eight recovered from losing the second-set tie-break to love to win 6-3 6-7 (0/7) 6-3 in Group A as the tournament began its fifth year in London.
At 28, Wawrinka has put together the best season of his career, capped by a first grand slam semi-final appearance at the US Open.
He beat Berdych in the fourth round in New York and it was Wawrinka, backed by a vocal Swiss support, who made the better start.
Berdych has been in the top eight in London every year apart from the O2's debut in 2009 but he was struggling with his serve and his movement was a little sluggish.
Wawrinka made the breakthrough in the sixth game and was rock solid until he came to serve it out.
At that moment the seventh seed's nerve wobbled but he eventually clinched it on his fifth set point.
Berdych improved at the start of the second set and Wawrinka did well to force a tie-break, fighting back from 0-40 in the eighth game.
The tie-break was dominated by the Czech, though, Wawrinka failing to win a single point.
The physical toll of the season was evident as Wawrinka called for the trainer to have his thigh massaged in the decider, but by then he was already back ahead.
A break in the fourth game proved enough, with Wawrinka clinching victory on his first match point when Berdych hooked a forehand wide.
With matches against world number one Rafael Nadal and third seed David Ferrer to come, the victory was crucial to the Swiss number two's hopes of making the semi-finals.