Del Toro's representative has confirmed that Stewart is pregnant.
"Kimberly is pregnant. Benicio is the father and is very supportive. Although they are not a couple, they are looking forward to the arrival of the baby," the Oscar winner's rep told Life & Style.
The baby would mark the first child for Del Toro and for Stewart, the daughter of singer Rod.
Stewart has previously been romantically linked to Laguna Beach star Talan Torriero as well as Jude Law and Rhys Ifans.
Del Toro, who is shooting his directing debut in Havana, is reportedly interested in taking on the role of a drug lord in Oliver Stone's forthcoming Savages.