Perez said he struggled to see the white line that marked the edge of the track.
It was moved at Turns 12 and 13 before Saturday’s action as part of the response to a potential safety issue with Pirelli’s tyres, although not all of the Mexican’s offences occurred at that spot.
The Red Bull driver started from the pitlane on hards after a change of chassis following his crash with Esteban Ocon and Nico Hulkenberg in Saturday’s sprint.
He rose to third before a first pitstop on lap 17, and was working his way back into the points when he received his first five-second penalty, which he had to take at his next pit visit. Perez later received another penalty that he took at his final stop. A third was then added to his race time, dropping him from ninth to 10th in the final results.
Perez insisted he had tried to avoid picking up any penalties but admitted he could have done a better job.
“It was, for me, impossible to see,” he said. “I was taking so much margin, giving up so much lap time for it, but I still got more.
“For me it was very difficult to judge, but there were drivers who were able to do that, so I don’t think I did a good enough job in that regard.
“But I also think it was a joke what we ended up doing with the track limits. First of all, I think that it is really bad that we come up with a solution last minute to police it. Then to start giving penalties away.”
He added: “It was very frustrating, as you can imagine. A really long afternoon, and I was very disappointed that I let my team down.
“It was a very poor weekend overall with the incident yesterday, which made it even worse today.
“Plenty of things to look at, and make sure we put everything in place for the coming races.”
Perez now has a lead of 30 points over Lewis Hamilton in the battle for second place in the F1 world drivers' championship and believes that he can hang onto it.
“Yes, and that is the absolute target,” he said when asked second place in the standings. “I have had a few bad races lately, but I think once we correct that, I should be able to re-find our form.”
A rare positive from the Qatar weekend was that Perez was able to add a new Honda power unit to his pool and avoid a further penalty due to his pitlane start.
That should help to ensure that he can contest the five final events, including his home race in Mexico, without picking up grid penalties.
