A furore erupted when Dawes took aim at the veteran for sitting out the drawn clash with South Australia that enabled the Bulls to qualify for the final.
Khawaja, set to be named later on Friday in the Bulls side for the Sheffield Shield final in Adelaide next week, called a press conference to offer an explanation.
He said a plan had been formulated with Cricket Australia medical staff and selector George Bailey to manage an ongoing hamstring complaint that he had played through in the previous round against Tasmania.
That game took place as Cyclone Alfred hit Brisbane, Khawaja leaving his young family to play and score a century despite batting in discomfort.
He said he hadn't spoken to Dawes, who said Khawaja had the all-clear from medical staff to play South Australia, in over a month.
"Joey said the medical staff had no idea; that is 100 per cent wrong," he said.
"I was talking to the Australian physio the whole time.
"Everyone knew about it ... that was one of the most shocking things ... categorically untrue.
"I don't do anything without talking to CA first. They always have final say."
Khawaja said he had texted Bulls coach Johan Botha to inform him of his original plan that was based around not playing back-to-back fixtures, but never got a reply.
The Test opener said it "felt like it would pop" in Tasmania, resorting to jogging while at the crease as they posted a vital nine-wicket win.
But at no stage was that management plan, or the injury, discussed with Botha or Queensland Cricket.
Khawaja, contracted to Cricket Australia, considered the situation under control until speculation swirled last week.
The 38-year-old then attended Melbourne's Australian Grand Prix, mixing photos of his time on the grid with one of him doing hamstring rehabilitation on his social media account.
On the Bulls' return to Brisbane on Tuesday, Dawes said he was disappointed by Khawaja's absence and "I have got a bunch of blokes here that all want to play".
Khawaja said he had Cricket Australia's blessing to attend the Grand Prix and was happy to mend his relationship with Dawes - a former Shield-winning fast bowler for the Bulls - after next week's final.
"I go home and curl up in a ball, or I go and watch F1," Khawaja said.
"I still look after my body. It's not by any coincidence I'm 38 and still playing.
"The optics look bad ... that's why I wanted to speak out.
"Just like Joey would have given; you give your heart and soul to this organisation," he said.
"I still do love Queensland Cricket, no matter what happens."
Khawaja has his sights set on continuing in Test cricket until the end of next summer's home Ashes series.
He captained the Bulls to their last Sheffield Shield title in 2020-21 when Australia teammate Marnus Labuschagne was man of the match with a brilliant 193 in an emphatic innings and 33-run defeat of NSW at Allan Border Field.
Labuschagne, who will captain the Bulls in the Shield final, was not concerned when he spoke earlier about the Khawaja situation.
He said the left-hander missing the final game in Adelaide and being available for the final was in essence "the perfect result".
"We understand if we want the best out of him he's going to need to make sure he's ready to go and fresh so he doesn't get himself injured," he said.
