While the justices ruled 7-2 in favor of Phillips, some media outlets downplayed the clarity of the decision.
They filed a successful complaint with the state commission and state courts sided with the couple, prompting Phillips to appeal to the top USA court.
While Kagan joined the majority opinion, she filed a concurring opinion along with Breyer that stated, "Colorado can treat a baker who discriminates based on sexual orientation differently from a baker who does not discriminate on that or any other prohibited ground".
Craig and Mullins won before the Colorado Civil Rights Commission and the state Court of Appeals, thanks to the state's inclusion of sexual orientation in its anti-discrimination law.
"Allowing discrimination against same-sex marriages would cause 'a community-wide stigma inconsistent with the history and dynamics of civil rights laws that ensure equal access to goods, services, and public accommodations", Justice Kennedy said.
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"I don't create cakes for Halloween", Phillips said.
"What matters is that Phillips would not provide a good or service to a same-sex couple that he would provide to a heterosexual couple", they wrote.
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"The reason and motive for the baker's refusal were based on his honest religious beliefs and convictions", Justice Anthony Kennedy wrote in the majority opinion. Kennedy cited comments by a member of the state commission who had said that religion was often used a basis for bigotry. She notably didn't agree that the Masterpiece case and the other bakeries' refusals were comparable, for a key reason: In one instance, the bakeries were refusing to make a cake because the language was offensive ― and they wouldn't have made that cake for anyone else.
Legal action followed after a baker refused to make Charlie Craig, left, and David Mullins a cake for their wedding.
In July 2012, Mr Mullins and Mr Craig went to Mr Phillips's Masterpiece Cakeshop in Lakewood, near Denver, to order a cake for a party to celebrate their planned marriage in MA later that year.
"Government hostility toward people of faith has no place in our society, yet the state of Colorado was openly antagonistic toward Jack's religious beliefs about marriage".
"We brought this case because no one should have to face the shame, embarrassment and humiliation of being told "we don't serve your kind here" that we faced, and we will continue fighting until no one does", they said.
Phillips, 62, owner of Masterpiece Cakeshop, was fighting for the rights of "creative artists" to choose what they will sell.
Justice Clarence Thomas wrote a concurring opinion in the case.
He appealed the state's decision, but lost in the Colorado courts.