Nike's decision comes a day after an online petition was launched urging the company to stop Pacquiao endorsing its products.
Pacquiao, revered in the Philippines for winning world boxing titles in eight different weight classes during his 20-year career, suddenly fell from grace after a 30-second interview on local television about same-sex marriage, which he opposes.
"It's just common sense. Do you see any animals of the same sex mating? Animals are better off, they can distinguish between male and female," Pacquiao told TV5 on Monday.
"Now if men are mating with men and women with women, then they are worse than animals," he said.
The 37-year old congressman, among those favoured to win a Senate seat at the May elections based on independent pollsters' surveys, apologised on Tuesday.
"I'm sorry for hurting people by comparing homosexuals to animals. Please forgive me for those I've hurt," Pacquiao said in a video message on his Twitter account. He said he remained against same-sex marriage.
Same-sex marriage is not allowed in the Philippines, where more than 80 percent of the 100 million population is Roman Catholic.
I'm sorry for hurting people by comparing homosexuals to animals. Please forgive me for those I've hurt. God Bless! pic.twitter.com/bqjRcWqp8R — Manny Pacquiao (@mannypacquiao) February 16, 2016
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