But he also noted - a win is a win.
"There are always things we can do better, no matter what game, but ... we still won," he said.
"It doesn't matter what you win by - you don't get any more points for winning earlier, later, even though it's nicer to win earlier.
"We know we could have been better in a few spots and we hope to improve that in the next game, but a win's a win.
"If you gave me the same result in this game, I'd take it."
Khawaja also said credit should be given to Pakistan for how well they fought out the game.
"We weren't playing at our best and they were playing very well, that's what it's all about," he said.
While the end was tighter than Australia would have liked, Khawaja said it was pleasing that they took control in the first innings.
"We led the game the whole way through, we sort of controlled it the whole way through," he said.
The heavy workload for the Australian bowlers in Brisbane has led to allrounder Hilton Cartwright being drafted in as cover.
"I can see where they're going with it," Khawaja said of the selectors' move.
"I don't know - there's so much that goes into it in terms of how the bowlers are feeling, what's happening, whether they are 100 per cent.
"Fast bowlers never seem like they're 100 per cent because their bodies go through so much.
"It will be up to the selectors, that's why they get paid the big bucks."
- AAP