Ledger died in January 2008 of an accidental prescription drug overdose. He was 28 and no longer with Williams at the time of his death.
Jonze, who is divorced from filmmaker Sofia Coppola, was the first man Williams dated after Ledger died, Usmagazine.com said.
However, the actress said in an interview for the October issue of Vogue that the relationship, which began in July 2008, ultimately didn't work out.
"The timing was impossible," Williams told the magazine. "I thought falling in love again was the only thing that was going to save me from the pain. This erroneous idea: It just makes things more complicated."
Williams said she also finds dating as a single mother difficult.
"I obviously don't know how to do it," she said.
"I was holding it together by a string and a paper clip in the fall and winter," she added. "I didn't know if I could keep it all together … You console yourself by saying it's all a deepening process. But it's weird. After the first year, the pain is less intense -- it's less immediate. But the magical thinking goes away, too. And that's a whole new reckoning."