The veteran actor handed out the final trophy of the night, at Sunday's star-studded event in Los Angeles.
But there was confusion when he abruptly announced the winner as Oppenheimer without first listing the nominees, as is customary.
"It was not my intention to omit them," Pacino said in a statement.
Instead, the 83 year old said, it was "a choice by the producers not to have [the nominees] said again since they were highlighted individually throughout the ceremony".
In his statement, which was issued on Monday afternoon, the Oscar-winning actor added that he "chose to follow" the way the producers wanted the award to be presented.
"I realise being nominated is a huge milestone in one's life and to not be fully recognised is offensive and hurtful," Pacino said.
"I say this as someone who profoundly relates with film-makers, actors and producers so I deeply empathise with those who have been slighted by this oversight and it's why I felt it necessary to make this statement."
Pacino's announcement meant the night ended on a confusing note, with none of the usual fanfare around the night's biggest prize.
Opening the envelope, he mumbled "my eyes see 'Oppenheimer'," leaving the audience momentarily confused as to whether the film had actually won.
BBC Culture reporter Emma Saunders, who was at the event in Los Angeles, said his announcement "had people sitting up in their chairs" as they tried to parse the information.
While it wasn't on the scale of the chaos at the end of the 2017 awards, when Moonlight and La La Land were mixed up for the best picture award, she said it gave reporters backstage "a panic attack right at the end of the ceremony".
Speaking about the presentation of the award in Variety, Oscars producer, Molly McNearney, said the decision to jump straight to the winner was made because "we were very worried that the show was going to be long".
McNearney, who is married to Oscars host Jimmy Kimmel, added: "By the time you get to the end of the show, you've seen all 10 best picture clip packages.
"People just want to hear who wins, and they're pretty ready for the show to be over. At least that's what we anticipated. So, we did not give him a clip package. We did not give him nominations to read."
Addressing Pacino, she apologised if the decision "put him in a tough spot".
"That made it a little confusing. But listen, that's the excitement of live television. You never know you're going to get exactly!"
The 10 films nominated for best picture were American Fiction, Anatomy of a Fall, Barbie, The Holdovers, Killers of the Flower Moon, Maestro, Oppenheimer, Past Lives, Poor Things and The Zone of Interest.
Oppenheimer swept the ceremony, winning best picture, best actor for Cillian Murphy, best director for Christopher Nolan, and best supporting actor for Robert Downey Jr.
An estimated 19.5 million people tuned in to watch Sunday night's 96th Academy Awards, according to broadcaster ABC.
That's the highest figure in four years, and nearly double the pandemic-era low. However, the ratings are still disappointing for a ceremony that regularly pulled in more than 40 million viewers a decade ago.
This year's Oscar nominations included smash hits like Barbie and Oppenheimer, that the public had actually seen, compared to the more esoteric and art-house films that dominated nominations at recent ceremonies. The Academy also moved the show an hour earlier this year, which may have helped to boost ratings.
Pacino, an acting legend, won the Oscar for best actor in 1993 for Scent of a Woman.
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