A day after rallying from a set down to beat 2008 champion Andy Roddick in the semifinals, Stepanek was forced to do the same against Fish while becoming the first Czech player to win the San Jose event since Ivan Lendl in 1983.
Stepanek got some help from his 27-year-old American opponent. Fish lost 10 straight points during one stretch in the third set, nine by unforced error.
"I came here with a lot of confidence and it just paid off," said Stepanek, who also won in Brisbane in January. "It's definitely, so far, my best [start]. This year I teed off right away in Brisbane and now this is my second title, which is great for me."
Stepanek broke Fish's serve twice in the final set, delivering the game-winner on an overhead forehand that caught Fish going the opposite direction.
That was in contrast to earlier in the match when Fish controlled the momentum with his powerful serve and kept Stepanek buried at the baseline. Fish, who went into the final with a tournament-leading 67 aces, had 16 more against Stepanek.
The turning point of the match came in the second set when Stepanek held serve to go up 5-4 then broke Fish to even the match and force a third set. Prior to that Fish had been broken just once in 45 service games.
"Until that moment Mardy was serving incredibly so I really didn't have many chances," Stepanek said. "I knew I had to stay with him, hold my serve and try to wait for my chances, which I believed would come."
Fish, who beat doubles partner James Blake in the semifinals, had seven aces in the first set including back-to-back winners to go up 3-0. Stepanek battled back to pull within 5-3 before Fish closed out the set, getting the winner on a 131 mph ace.
Fish trailed 3-2 in the second set when Stepanek called a medical timeout to have his left leg tended to. The interruption didn't last long but it seemed to throw Fish off his rhythm and allowed Stepanek to gain the upper hand.
Though Fish held his serve when play resumed, he won only one other game in the set and began to make numerous unforced errors. After Stepanek held serve to go up 5-4, Fish walked around behind the baseline muttering to himself and let out an audible groan.
"If you put a tally on how many times he calls the trainer, it would be pretty high," Fish said. "He seemed fine to me. I would be shocked if I was up a set and he didn't call the trainer."
Stepanek broke Fish's serve in the ensuing game to tie the match at one set apiece then dominated the final set, winning the final four games.
Afterward as he celebrated, Stepanek donned a San Jose Sharks jersey and paraded around the court. He dropped to the ground briefly for a mini-version of the worm dance he has become known for, then jumped to his feet and held his arms in the air as the crowd applauded.