Roddick was forced to dig deep after throwing away a substantial second set lead before finally beating the Czech 7-6 7-6 at the Pat Rafter Arena. Everything looked to be going smoothly for Roddick, playing his first tournament since a knee injury cut short his 2009 season last September.
He won the opening set in a tiebreak after all games had gone with serve and opened up a commanding 5-1 lead in the second before he suddenly got the wobbles.
He twice failed to serve out the match as Stepanek forced a second tiebreak then faltered again as he neared the finish line.
Roddick made a great start and built a 6-1 lead to have five match points, but he blew the lot before eventually winning 9-7.
"It was weird. I don't think I have squandered a lead where I have been putting in first serves and making approach shots," Roddick said.
"And in the breakers it was the same deal. I kept making first serves so that was helping me hold on to the last shred of sanity I had.
"But at the end of the day the only thing that will be remembered is the 'w' (win)."
"I certainly don't know if I expected to win my first tournament after a pretty extended lay off. I feel pretty good about it," Roddick said.
"I never gave up. I was fighting until the last point," he said.
"I said to myself 'you are in Brisbane, you won here last year, there is something special here', but in the end it wasn't good enough.
"(But) back to back finals -- it has been a magic place for me here. I will be coming into the Australian Open with only positives."
(Reporting by Julian Linden; Editing by John O'Brien)