Canadian Shapovalov fell short in a valiant comeback bid against all-time great Nadal, who eventually won through 6-3 6-4 4-6 3-6 6-3 after over four hours on Rod Laver Arena.
The 14th seed was left fuming between the first and set second, though, when he felt a time violation should have been given after Nadal made him wait for play to resume.
"Started the clock so long ago, he's still not ready to play. You've got to call him," Shapovalov said to Bernardes.
After Bernardes opted against doing so, Shapovalov said: "You guys are all corrupt."
"I think I misspoke when I said he's corrupt or whatever I said. It's definitely emotional, but I do stand by my side. I think it's unfair how much Rafa is getting away with," Shapovalov told a news conference when asked about the incident.
"I mean, I'm completely ready to play and the clock is ticking three, two, one, clicking towards zero, and I'm looking at the ump, and obviously I'm going to speak up and say something.
"I've been ready to play for a minute and a half, and he tells me he's not going to give him a code violation because I'm not ready to play. To me, it's a big joke if somebody says that."
Shapovalov was further frustrated ahead of the deciding set where Nadal left the court for a medical check up having struggled with a stomach issue and also had a toilet break.
The 22-year-old felt the extended break quelled his growing momentum and that the elite players have different boundaries.
"And then after the fourth set, the guy goes – and for the same thing last year I wasn't allowed to take a toilet break when I asked for a medical," he added.
"He had already taken two medicals. He was getting medically evaluated, that's what the ump said after the fourth set, getting medically evaluated, and after the evaluation the guy goes and takes a toilet break.
"It's like, where is the line? Where are you going to step on the players and again, I respect everything that Rafa has done and I think he's an unbelievable player.
"But there's got to be some boundaries, some rules set. It's just so frustrating as a player. You feel like you're not just playing against the player; you're playing against the umpires, you're playing against so much more.
"It's difficult. I mean, it was a big break after the fourth set for this reason, and the momentum just goes away. It's much more difficult to play, I think.
"Again, not trying to say anything against Rafa; he's a great player, I really respect all he's done, but I just think it's super difficult and super frustrating as an athlete to go up against all of this."
Asked if he feels Nadal gets preferential treatment, he added: "Of course. 100 per cent he does. 100 per cent. Every other match that I have played, the pace has been so quick because the refs have been on the clock after every single point.
"This one, after the first two sets it was like an hour and a half just because he's dragged out so much after every single point. He's given so much time in between sets and all this. It's just dragged out.
"Like I said, for the same reason I wasn't allowed to go to the washroom last year at the Australian Open because I had called a medical. I'm not arguing the fact that he had a medical or whatever it is. But how can you get evaluated medically and have a toilet break at the same break and just causing so much delay in the game?
"I mean, it's just not balanced."
Shapovalov and Nadal had a discussion at the net, but the former explained that it was an amicable exchange.
"It was nothing against Rafa. Rafa was serving and I would expect the umpire to be looking at Rafa and the umpire was staring me down. It didn't make sense to me," he said.
"Rafa is getting ready to serve, there's a clock right there, as an umpire you should be looking at the server. The guy is staring me down so I just looked at him like, 'Why are you looking at me?'
"It was shortly after I had said – obviously, like I said, I misspoke, but he was staring me down, so I felt like there was some feud or something. I looked at him.
"I was just explaining that to Rafa that it had nothing to do with him."