Judge George H. Wu's order went into effect Thursday, a month after he approved the fund and released all parties from further liability.
The case will move to state court, where a judge will hear testimony from victims of the 2008 crash before deciding how to divide the money.
The collision of the Metrolink train and a freight train killed 25 people and injured more than 100. Investigators believe the Metrolink engineer provided by Connex was texting moments earlier and ran a red light.
Metrolink and Connex, a subsidiary of Veolia Transportation, agreed to the sum, the maximum for a passenger train wreck under U.S. law.