Team chief Martin Whitmarsh, who also denied weekend claims that he was considering resigning after the team's poor start to the season, said that Mexican Perez was told to slow and preserve his tyres in the final stages of the race.
But he said this was only to ensure he finished and had nothing to do with any fears that me might launch another attack on Button, the 2009 champion, in the closing laps.
The pair finished eighth and ninth in the first European race of the season three weeks after their battle in Bahrain.
Whitmarsh said: "Checo (Perez) himself said at the end his tyres were finished.
"What we didn't want was him to be battling until he ran out of rubber. He very nearly did as it turns out. So it was not tactical, it was practical.
"It was a fair fight, but if you are asking - did we ask him to back off and not fight? No, not at all. We could see the tyre wear energy and we were worried he was going to end up with no rubber at the end of the race, which he virtually did."
Whitmarsh added that the double points haul in Spain was a small bit of good news on an otherwise difficult weekend, but was still not good enough for McLaren.
"We are fighters so we try to get more positions than we get in qualifying," he said. "We are not quick enough. We need to work harder and that is what we have got to do. Overall both drivers did a good job."
Perez used his Twitter account on Monday to keep the record straight. He said: "..just want to tell everyone the radio message I had was all about to save the tyres. Never a team order -- can't wait for Monaco."