The Mexican put his car seventh on the grid, equalling his best starting position of the year, while Button was 13th fastest with an additional three place drop for ignoring a red flag on Friday.
There was a notable tension in the McLaren hospitality after qualifying as Perez, who is being replaced by 21-year-old Dane Kevin Magnussen, and team principal Martin Whitmarsh sat side-by-side in front of the media.
It was left to Whitmarsh, flanked by Perez on one side and Jenson Button on the other, to defend his late decision to replace the 23-year-old Mexican.
"You reach a point where decisions fall into place," Whitmarsh told reporters. "There is no particular calendar necessary for that and in reality we made the decision formally this week.
"This has been a tough year for the team, it's been a tough year for Jenson and Checo (Perez). They fought through a very difficult year. I'm not happy that we've given them a season like that.
"When you hire a rookie there is some risk in that but we wouldn't have done it if we didn't think it would pay off," he added.
"We made a decision and hope Kevin can live up to expectations of the team."
Asked if he was motivated on Saturday to deliver the type of effort that might make McLaren regret their move, Perez again repeated the view that his departure was a business decision made by team while Whitmarsh stared straight-ahead with little expression.
"It's no secret I am going through a tough time," conceded Perez, who will end his one year at McLaren after next week's finale in Brazil. "I'm leaving the team, it came as a shock to me, I didn't expect it at all.
"I always thought I was going to stay on board but this is Formula One and things change very quickly.
"I don't know where I am going to end up, I hope I find a seat that motivates me to stay in Formula One, if not I have to look for other options."
With few competitive seats available and those being hotly contested, Perez admitted he might have to pursue some options away from Formula One.
He ruled out a move to NASCAR but left the door open to trying his luck in IndyCar if nothing was available to him on the world's grand prix circuit.
"I will not be in Formula One just to be here. I really need to find a competitive seat that can give me the opportunity to keep showing my talent and fight for a championship," said Perez.
"I haven't had any contact, my head is in Formula One but if I don't find the right seat for my future I might have to look to that option."
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- Motor Racing
- Martin Whitmarsh
- Jenson Button