Police said they were called to an incident at 5.38am on Saturday after six horses escaped from a nearby field and got onto the motorway’s southbound carriageway near Horbury.
Officers were called after two of the animals had been hit by a Vauxhall Corsa.
One horse died at the scene while another was seriously injured and had to be put down by an armed officer, police said.
The driver was not hurt and the remaining horses were safely returned to a field.
A West Yorkshire Police spokesman said: “The motorway was closed for a short period while the dead horse was removed from the scene but a local diversion between the two slip roads was put in place to keep disruption to a minimum.”
Inquiries are continuing into the incident, which happened near junction 39.