A source told the magazine the romance couldn't survive the long distance and the couple ended it this month.
Segel recently signed up for a ninth and final season of the TV sitcom "How I Met Your Mother," which will keep him in Los Angeles.
Williams lives with Matilda, her 7-year-old daughter, in Brooklyn. The little girl's father is the late actor Heath Ledger, who died in 2007 of an accidental drug overdose.
Humongous iceberg slowly drifts away from Antarctica
Jeb Bush 'thinking about running for president' in 2016