The Oscar-winning pair holidayed in Hawaii over the festive period and were photographed sitting on the beach near his holiday home.
Into The Wild star Sean showed off his surfing skills in the waves while the Prometheus actress went for a dip and worked on her tan.
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They were joined by a male friend on the beach once Sean had finished surfing.
A source told the New York Daily News that they looked "very close and comfortable together."
The South African actress, who travelled to the island without her adopted son Jackson, was rumoured to be staying at Sean's beachfront house.
The pair, who have been romantically linked several times in the past, flew back to LA together on Wednesday evening.
"Charlize and Sean have been friends for years," a source told PEOPLE magazine. "They have been spotted out together several times in the past few years. Even when Charlize was dating Stuart [Townsend]. They both had dinner with Sean several times."
Despite claims that Sean was just helping Charlize through her split from the Irish actor, they were romantically linked again in 2011.
Most recently the pair attended Family Guy actor Seth MacFarlane's festive party together.