Organising committee chairman Beattie has apologised for the decision to have athletes enter the venue before the broadcast began, which denied inspirational para-athlete Fearnley the chance to carry the flag in front of a television audience.
The move prompted anger towards organisers, particularly from presenters for broadcast rights holders the Seven Network, while the ceremony has been labelled overall as underwhelming and lacking star power.
Fearnley, who received a rousing ovation as he led the Australian team into the stadium on Sunday hours after winning gold in the men's wheelchair marathon, agreed with Beattie that organisers had "got it wrong".
But he stopped short of any further criticism.
"Right now, we have just finished the best and most inclusive Games we have ever had," Fearnley told SEN radio.
"It's the best two weeks of my life ... Let's just move on and remember the Games as the absolute success that it was.
"There were too many things to celebrate to get caught up on that."
Beattie said the decision was made to limit the time athletes, many of whom were fatigued from competition, had to wait outside the stadium.
"Having them come into the stadium in the pre-show meant the TV audience were not able to see the athletes enter the stadium, alongside flag bearers. We got that wrong," he tweeted on Monday.
"This decision to bring the athletes into the stadium before the broadcast was operationally driven given there were restrictions on being able to keep the athletes waiting in comfort.
"We were driven by the welfare of athletes."
Further Australian athlete reaction has been mixed, with star swimmer Cameron
McEvoy unaware of the furore until Monday, but Boomers basketballer Angus Brandt saying they felt "left out".
Opening ceremony flagbearer Mark Knowles admitted it was a disappointing way to mark his retirement from hockey.
"That part was a little bit, you know, not what the athletes would have liked," he told Fox Sports."
"It's hard to fault these Commonwealth Games and I'm very, very cautious of saying anything that would put a dampener on what the athletes did."
"One little event last night, people still loved it, but I think they would have loved it even more."
Beattie also conceded speeches went for too long.
The former Queensland premier did the rounds on breakfast television to take full responsibility - rejecting criticism directed at the American producers of the ceremony, Jack Morton Worldwide.
Seven presenter Johanna Griggs, a 1990 Commonwealth Games swimming bronze medallist, teed off at organisers after viewers initially expressed frustration with the broadcaster when athletes were left out.
"They made a decision not to have athletes enter the stadium they made the decision not to show the flagbearers," Griggs said on Seven on Sunday.
"I'm furious. Actually wrecking a tradition that is so important."
"You want to see the athletes come in. You want to see them jumping in front of camera. You want to see them celebrating 11 days of great sport."
"We missed out on all of that."
Large sections of Carrara Stadium seating were empty while a number of athletes slipped away to the bar before the ceremony had reached its halfway point.