The 27-year-old American beat Frenchman Richard Gasquet in the quarterfinals Friday night and endured a 2-hour, 8-minute semifinal against Berdych in humid conditions starting about 14 hours later.
Roddick dropped serve twice against Berdych in the opening set, when he didn't convert any of his four break-point chances. It was the first time in the tournament that his serve had been broken, ending a run of 30 straight winning service games.
He rebounded in the second set, building a 3-0 lead with an early break. The third set was on serve until Roddick broke for a 5-4 advantage.
"I like to confuse and conquer sometimes," Roddick joked of his first-set lapse. "I didn't feel like I was hitting the ball that badly, but he played really well.
"The biggest part of the match was the first couple of games of the second set, where I didn't want to let him keep rolling ... to stop the momentum early in the second."
Roddick was playing singles and doubles here in his first tournament since he injured his left knee in October, hoping to improve his conditioning before the Australian Open starts Jan. 18 in Melbourne.
Soon after his singles win Saturday, he joined James Blake for a doubles semifinal, but the American pair lost 6-4, 3-6, 13-11 to Frenchmen Jeremy Chardy and Marc Gicquel.
The French pair will meet top-seeded Lukas Dlouhy and Leander Paes in Sunday's final.
Now, Roddick can focus entirely on trying to win his 28th ATP singles title.
"I wanted to come here and play well, get better with each match and get matches in," he said. "That's my biggest thing. I'd love to win here. The goal is to be prepared for Melbourne and I feel like that has been accomplished for the most part.
"Now the business end of the tournament, you want to try to go as far as you can."
Stepanek easily beat Frenchman Gael Monfils 6-2, 6-1 in an hour in the first semifinal.
Monfils seemed dazed by some of Stepanek's returns, shaking his head in disbelief several times and tapping his racket against his forehead. He also seemed to be bothered by a bandage on his right shoulder.
Trailing 5-0 in the second set, Monfils looked upward and smiled when he finally won his first game of the set.
"When I broke him to go 4-0 up in the second set ... I think he knew breaking me twice to get back into the match would be a very difficult thing," Stepanek said. "I think I also broke him mentally then."
The men's final will be Sunday. The all-Belgian women's final between Kim Clijsters and Justine Henin is scheduled for Saturday night.