The Oscar-winning "Argo" filmmaker is also a recovering alcoholic who spent time in rehab in 2001.
UsMagazine.com said Affleck went to offer his support to Lohan during her recent stay at Cliffside Malibu Rehab Center, assuring her the entertainment community stands behind people who make a real effort to stay clean.
The two did not, however, discuss the possibility of Lohan appearing in Affleck's upcoming film "Live By Night," contrary to media reports claiming they did, the magazine said.
Lohan, 27, was under court order to undergo in-patient treatment for substance abuse as part of her conviction for reckless driving and lying to police.
She checked into the Betty Ford Center May 3 but reportedly was unhappy with her treatment and requested a transfer to Cliffside Malibu.
The "Mean Girls" and "Freaky Friday" star's once-bright career has been eclipsed in recent years by her battles with drug and alcohol addiction, motor vehicle offenses and other legal woes.
The Oprah Winfrey Network is paying the troubled actress about $2 million to star in an eight-part docu-series about her efforts to remain sober and revive her flagging career.