The decision to promote O'Connor comes two years after the Marlins made history when they named Kim Ng as Major League Baseball's first female general manger.
"I think we're a really special organisation. (Team owner) Bruce (Sherman) has put a lot of trust in us, and he really looked at merit and who can do the job," O'Connor said in a report on the Marlins website.
"I'm really excited about it. I think it makes our organisation unique and stand out, and shows what women can do and the roles that they can hold."
In her new role, O'Connor's responsibilities will include overseeing sales, partnerships, marketing, human resources and diversity, equity and inclusion and special projects.
"We are fortunate to have someone with Caroline's business acumen and vision leading our day-to-day business operations," Sherman said in a statement. "Her passion and drive for success is unmatched in our game and the South Florida market.
"Her leadership will continue to guide the Marlins organisation toward our goal of sustained success while strategising additional new ventures to grow our business and enhance our brand recognition."