Commissioner Katarina Carroll made the apology at a private ceremony attended by Brisbane Pride leaders and police who are part of the LGBTIQ+ community.
After the ceremony at the Brisbane Police Headquarters on Friday, a rainbow police flag was raised outside.
Consensual sex between men was illegal in the state until 1991 with 464 charged with crimes of that nature and thousands of people, including officers, have been bullied and abused because of their sexual orientation from the police force.
Ms Carroll's historic statement of regret comes 15 months after Brisbane Pride asked uniformed police officers not to march at its annual festival in Brisbane because of the lack of an apology.
"We must acknowledge for much of its history, the QPS inflicted profound pain upon Queensland's LGBTIQ+ people by enforcing laws that criminalised homosexual activity between consenting adults," the commissioner said in her speech on Friday.
"As you would appreciate, it has been an extremely emotional and challenging time.
"To all those directly and indirectly impacted by the discrimination and prejudice from these laws, which were enforced by the QPS, I am sorry for this profound hurt and pain.
"I am also sorry to those within our own organisation who experienced discrimination and prejudice."
Brisbane Pride president Bec Johnson said it was important to acknowledge LGBTIQ+ community members who were no longer alive, but who had bravely protested against police mistreatment, bashings and death threats.
She said it had been challenging to remember the days when police officers threatened to arrest people for kissing or holding hands or attacked them with hate speech and physical violence.
"Today we remember the legends that came before us," Ms Johnson said.
"We acknowledge and stand here in solidarity today with those members of our communities who have survived.
"Both those in the room and those across the state will hear this apology today and will remember their experience. We have hope that this brings you some peace."
Queensland Parliament apologised for the laws criminalising homosexuality in 2017, but the LGBTIQ+ community has been pushing for the Queensland Police Service to say sorry for historic mistreatment.
Revelations the QPS was investigating a Facebook group where police were making sexist, racist and homophobic posts in September 2021 spurred Brisbane Pride to ask uniformed police to stop matching at its festival.
Ms Johnson said that collective action had opened a constructive and meaningful dialogue with the QPS that had culminated in the long-awaited apology.
She said the Brisbane Pride committee had since passed a motion affirming support for police officers marching in the festival.
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