In a column for 'The West Australian' newspaper, Johnson questioned Warner's inclusion in the 14-member squad for the three-match Test series against Pakistan starting in Perth on December 14.
Johnson wrote that Warner, 37, doesn't deserve a place in the squad going by his form or merit, and he has not taken full responsibility for his role in the 'sandpapergate' ball-tampering scandal in South Africa in 2018 for which he was banned for a year.
Khawaja backed Warner, his opening partner in Test cricket, and Steve Smith, who was the Australia captain during the infamous scandal.
"Warner and Smith are heroes in my mind," Khawaja told reporters on Monday.
"They missed a year of cricket through dark times. No one's perfect. Mitchell Johnson's not perfect.
"What they (Warner and Smith) have done for the game -- how they have grown the game -- far outweighs anything else they have done.
"To say Dave Warner or anyone else involved in sandpaper (gate) is not a hero... I strongly disagree because they have paid their dues. A year out of cricket is a long time," he added.
Khawaja also disagreed with Johnson's view that chairman of selectors George Bailey was too close to Warner.
"I'm not sure you can argue with that. (The criticism) is harsh," Khawaja said.
But former Australia Test captain Tim Paine feels Johnson had made some good observations about Warner's form.
"David hasn't been playing well and would other people be getting the run he's getting now? Probably not," Paine told SEN Radio.
"But in my opinion, he's (Warner) got credits in the bank because he is one of the all-time greats.
"I think you can read between the lines that (Johnson) and Davey don't get along."