The goalkeeper was first saved by James Perch when he fumbled a shot, and then later there was a dodgy penalty decision that went Newcastle's way.
United beat Atromitos 1-0 in the second leg of their qualifier last night, giving them a 2-1 aggregate victory.
The Greek side should have had a penalty late in the first half after Krul clipped Chimbinho as he attempted to reach for the ball.
However, referee Stephan Studer booked Da Silva for diving.
Atromitos had another penalty claim rejected in the second half, and Elini Dimoutsos’s shot narrowly wide from 10 yards in a nervy finale.
Tim Krul: “Sometimes it doesn’t matter how you do it.
“Sometimes you don’t deserve a clean sheet, and you get one, and sometimes you deserve a clean sheet, and don’t get one.
“We didn’t deserve this one. We were a bit lucky, especially with the incident in the first half.
“Sometimes you have to take that – you ride your own luck.
“I’m glad (the referee) saw my side, but it was a tricky one. I think he tried to make the most of it – that’s what the referee was saying.
“I did get a touch on him, but he tried to make the most of it. That’s why he gave him a yellow.
“It’s fantastic – it’s where this club deserves to be, and I’m looking forward to the draw.
“I want to be in these nights. It’s fantastic to be in Europe.
“Nobody really knew anything about this team, but they’re a decent side. It’s a great experience. These kind of nights will make us stronger.
“We’re just looking forward to it. It’ll be a fantastic experience.
“We’ll see what happens. The most important thing is that we’re in the draw."