The hard-throwing reliever left the Yankees on Monday after his father collapsed at home in Nebraska, and the pitcher was placed on the bereavement list.
Harlan Chamberlain is hospitalized at St. Elizabeth Regional Medical Center in Lincoln.
"His father is a little better," Girardi said before Tuesday 5-3 win against Tampa Bay. "Still more tests to be run. Joba is by his father's side. We're just praying that he gets better quickly."
Girardi said Chamberlain will miss the two-game series against Boston that begins Wednesday night at Yankee Stadium.
"He understands the important thing is to be there," Girardi said. "Take care of pop. His father has been through a lot in his lifetime. You only have so many days with the people you love. You've got to make sure you're where you're supposed to be."
Harlan Chamberlain had polio when he was 9 months old and uses a motorized scooter. He is deaf in one ear and without full use of his left arm.
Harlan Chamberlain raised Joba as a single dad. He attended New York's season opener this month and was at last week's series in Kansas City.