"I sincerely apologise. Nobody's personal life is my business," tweeted the 36-year-old, who is best known for her role in the US version of The Office and films including I love you man and The Social Network.
Rashida's apology came after she made comments about John's rumoured homosexuality to website Spinning Plates yesterday.
"It's time … like John Travolta? Come out! Come on. How many masseurs have to come forward? Let's do this," said the actress.
Fifty-eight-year-old John, who has a family with wife Kelly Preston, was targeted by lawsuits earlier this year after two male masseurs claimed he had sexually assaulted them.
A former assistant to John also claimed he had a six-year relationship with a male pilot in the '80s.
Rashida's rant about the actor came as she congratulated other celebrities including
Frank Ocean and Ricky Martin for coming out.
"Big stars need to come out. Ricky Martin was huge. That was big; I was really happy about that," she said, adding, "People are so precious about their careers."
Being precious versus making embarrassing public apologies? We know which one we'd choose!