Guan, at 14 the youngest ever player at Augusta, was given a one-shot penalty on the 17th hole after previously being warned that he was taking too long over his shots.
That meant his par on the 17th became a bogey five and a round of 75, but the 14-year-old's four-over total of 148 proved good enough to make the halfway cut thanks to being within 10 shots of leader Jason Day, who shot a best-of-the-day 68 to finish six under.
The rules state that players will be told when they are out of position on the course, then advised they are being put on the clock and if they subsequently receive two "bad times", are liable to be penalised.
Guan was warned on the 10th, started being timed on the 12th and then took too long over his second shot to the 13th and approach to the 17th.
"I respect the decision. This is what they can do," Guan told ESPN. "I think they should do it with respect to everybody."
John Paramor, the European Tour's chief referee who gave Guan the penalty, said: "I feel like that in those situations, any time they happen, that's my job. That is what I do."
Asked if Guan's age affected his decision, Paramor added: "No, because it is the Masters."
Guan said he had been handed his penalty after the windy conditions on Friday prompted him to take time over his club selection on the 17th.
"We had some rain early in the round and the wind switched a lot and it goes hard. I just had to make that decision, I switched my club," he said. "Unfortunately it is my second bad time.
"It did affect me a little bit on the putt on the 17th and I didn't make it. It was still okay. On the 18th I did pretty good to save the par."
Tournament organisers confirmed Guan's penalty in an official statement in which they said he had "exceeded the 40-second time limit by a considerable margin".
Slow play is a constant problem in professional golf yet rarely penalised - the group including Tiger Woods took five hours 45 minutes to play their round - so Guan's plight met with considerable sympathy, not least from playing partner Ben Crenshaw.
"This is not going to end pretty. I'm sick for him," two-time Masters champion Crenshaw said. "I feel terrible. He is 14 years old. I'm so sorry this has happened.
"When you get the wind blowing out here, believe me, you're going to change your mind a lot. It is not easy to get around this golf course the way it's set up for two days.
"There's no question he played slowly at times. But he was working things out. The rule's 45 seconds (sic) and it's pretty difficult for somebody to do that in a tournament like this with conditions the way they are.
"It's going to happen, but I'm really sorry. This is not pretty."
Italy's Matteo Manassero, who had been the previous youngest Masters competitor at 16 and was also playing with Guan, admitted the teenager had been slow.
"I think it's the biggest thing he needs to be careful about, because I think he's ready," Manassero said.
"When the caddie pulls the club for him, I think he's ready. But most of the times that he takes a little too long he just asks questions that I think he knows, but just to be sure, just to be clear in his mind.
"We all feel sorry, but this is the way professional golf goes. This will end up being a great experience for him.
"We all hope he's going to make the cut, but this certainly will be a very valuable lesson. He will never forget it for sure, and he will learn from it."