A Nike statement said the company had severed its ties with Pacquiao, who triggered a firestorm of controversy with his comments to a Filipino broadcaster earlier this week.
"We find Manny Pacquiao's comments abhorrent," a Nike statement said.
"Nike strongly opposes discrimination of any kind and has a long history of supporting and standing up for the rights of the LGBT community... we no longer have a relationship with Manny Pacquiao."
The devoutly Christian Pacquiao, 37, had issued an apology soon after the controversy erupted.
"I'm sorry for comparing homosexuals to animals. Please forgive me for those I've hurt," Pacquiao said in a video post on Instagram, his arms crossed.
Pacquiao said he was not condemning homosexuals but was standing by his conservative Christian faith.
"I love you all with the love of the Lord. I am praying for you."
Pacquiao told television station TV5 earlier this week: "It's common sense. Do you see animals mating with the same sex? Animals are better because they can distinguish male from female."
"If men mate with men and women mate with women, they are worse than animals."
Gay marriage is outlawed in the Philippines due to strong opposition from the Catholic Church and 80 percent of the country's 100 million people subscribe to the faith.
Gay marriages are officiated at small churches but are not recognised by the mainstream church or the state.
However Pacquiao's remarks drew revulsion from some of his compatriots, with the country's most popular gay comedian, Vice Ganda, urging his 6.7 million Twitter followers to "#PrayForMannyPacquiao".
"Some people think they can judge people, like God, just because they've attended a prayer meeting and read the Bible," he said.
Jason Collins, the first openly gay athlete in the NBA, dismissed Pacquiao as "bigoted."
"I lost all respect for you," Collins wrote on Twitter. "Bigoted people like you ( and yes you are one) should never hold an office in politics."