But the Frenchman was still unable to take his opportunities and instead it was Murray who struck - breaking twice in quick succession as mistakes began to creep into Simon's game.
In the end it was a comfortable win for Murray, who can relax ahead of his match with Federer knowing he is already into the last four.
"The first two matches were really important," Murray told BBC Sport. "I did not want to go into the final day having to play Federer to qualify.
"I have played really well so far and I have a chance to win the competition. I would have signed up for that at the start of the year, that is for sure."
Murray was noticeably sharper than he was against Roddick and feels he is in good shape to continue his progress.
"My first match really helped," he explained. "I'd been falling asleep around 8pm in the evenings most days and that match started at that time. I felt tired, and my legs were very heavy after some long rallies but today I felt absolutely perfect.
Any time you play against Federer, who is probably the greatest player of all time, it is probably a bit disrespectful to not try to win
"I have got a lot of confidence just now and I want to try to keep it going. I have got a great record indoors and I really like these courts."
Serbia's Novak Djokovic became the first player to book his semis place on Tuesday after beating Nikolay Davydenko in three sets in the Gold Group, and Murray has definitely joined him.
Federer needed a win over Stepanek otherwise he would have been out of contention before meeting Murray in his final match on Friday.
On paper it seemed an easier task for the Swiss star than overcoming Roddick but he had to work hard to take the first set on a tie-break.
Stepanek also pressed him hard in the second before folding at the end - losing the match thanks to a double-fault which saw him drop his serve to love.
Federer revealed afterwards that he had been ill since Monday evening, explaining: "I guess I got really lucky that the match was scheduled late. Then that Andy pulled out made it a little bit more lucky.
"And then Radek is not playing with his own racquets, so that made it a little bit more lucky again," he said.
Federer was not at his best but has had to overcome a stomach upset
"At the end of the day I still have a chance. I hope with a day of recovery, I'll make a miracle happen here and get through into the semis."
A victory for Murray on Friday would eliminate Federer and he says he will not lack motivation against the top seed.
"I'm sure the tournament director would rather I didn't want to win that one," Murray laughed.
"But I think any time you play against Federer, who is probably the greatest player of all time, it is probably a bit disrespectful to not try to win.
"I will give it my best shot. There is a lot of pressure on him to win that match and I will just try to do my best.
"Maybe I will feel too relaxed and I won't play my best because there is not that much pressure on me but, in terms of actually wanting to win the match, not too many people beat three top ten players in the world and go through their group stage in the Masters Cup without losing and I would love to do that."
On Thursday, Djokovic, who has already qualified, takes on Jo-Wilfried Tsonga in a dead rubber, with the winner of the Davydenko and Juan Martin del Potro clash progressing from the Gold Group.
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