Batsman Pujara completed an innings of 193 on Friday as India scored 622 for seven declared to pretty much end Australia's hopes of the victory they need to save the series.
The 30-year-old rarely looked under any threat as he ground out his third century of the series on a track which offered virtually nothing for pace or spin to take took his tally to 521 runs over four tests.
"It's one of those things we can't control, we just have to deal with it the best we can," Paine said of the wicket.
"What I do know is that the pitch here, and the pitch in Melbourne, didn't make us bowl and bat as poorly as badly as we have in this test.
"We've just been outplayed and both teams have had similar conditions.
"I'd like to see a bit more bounce and a bit more pace but we've just got to play better on whatever wicket is served up wherever we play in the world."
Pujara only managed scores of 24 and four in the one test that Australia won and Paine suggested that the drop-in wicket at the new Perth Stadium might have had something to do with it.
"In the form he's in at the moment, he's not missing too many," Paine said.
"When the wicket is like it is at the moment and you can't swing the ball, not many good players miss them. He's been really patient and disciplined around his off-stump.
"We've tried to bounce him, we've tried wide of the stumps, we've tried at the stumps, Nathan Lyon's been over and around ... and he's been too good for us.
"Having said that, I thought in Perth, when we got some bounce in the wicket, we saw where we can get him out. Caught behind the wicket. Twice."
Paine admitted that the number of overs the Indian batsmen had forced them to bowl in Melbourne and Sydney had taken its toll on his attack and that paceman Mitchell Starc was struggling with confidence.
One thing that could not be doubted, though, was that the Australians were giving their all and that would continue when they resumed on 24 without loss on Saturday.
"The easiest thing to do is to throw in the towel but we won't be doing that," he said.
"We'll be turning up tomorrow and trying our guts out to get back into this game."
(Reporting by Nick Mulvenney, editing by Amlan Chakraborty)
