The "Ally MacBeal" veteran, who met Ford in 2002 and married him in 2010, had arrived at the emergency room shortly after her husband did, a source told People.
"She looked concerned and stayed with Harrison until late last night," the mag's source said.
Flockhart, 50, reportedly took their teenage son, Liam, to school Friday morning and then headed back to the hospital.
The 72-year-old "Indiana Jones" and "Star Wars" actor was, according to his rep, "banged up" in the crash, which happened shortly after the single-engine plane took off from Santa Monica Airport. The seasoned aviator managed an emergency landing -- not his first -- on Venice's nine-hole Penmar Golf Course.
"The injuries sustained are not life-threatening," the rep told the Los Angeles Times in a statement. According to Gossip Cop, Ford suffered a broken ankle and broken pelvis.
"Where am I?" the actor had asked as bystanders worked to get him out of the wrecked plane, according to a witness who talked to L.A. Now. Ford's face and body were covered in blood, and fuel was leaking from the vintage aircraft.
Son Ben Ford was also quickly with his dad in the ER, tweeting out Thursday, "At the hospital. Dad is ok. Battered, but ok! He is every bit the man you would think he is. He is an incredibly strong man."
He also thanked well-wishers for their "thoughts and good vibes."