Jones, 39, was fatally shot on Wednesday when a gunman opened fire inside the museum.
Authorities say the gunman was 88-year-old white supremacist and Holocaust denier James von Brunn, who on Thursday was charged with murder. Von Brunn could face the death penalty.
In a statement Wednesday, Mr. Obama said he was "shocked and saddened" by the event and praised Jones.
"Today, we have lost a courageous security guard who stood watch at this place of solemn remembrance," he said. "My thoughts and prayers are with his family and friends in this painful time."
The Holocaust Museum reopens today, with a makeshift memorial with flowers and a photo of Jones formed outside of the building. The museum was closed on Thursday in memory of Jones.