Prosecutors have ordered an autopsy be carried out on the remains, police in the federal state of Rhineland-Palatinate said in a statement.
BASF firefighters were caught in an explosion on Monday after responding to a small blaze near docks where tanker ships unload flammable liquids and liquified gases via systems of pipes.
Two firefighters were confirmed dead on Tuesday, with one person missing and more than 20 hurt, including six seriously.
The body found on Wednesday is believed to be that of the missing person.
"We have to assume that our fears have become a tragic certainty and lament a third death," BASF board member Margret Suckale said in a statement.
Monday's blast sent smoke billowing into the sky above the company's home town of Ludwigshafen and neighbouring Mannheim, with emergency responders called in from the whole region to fight the resulting blaze.
Local people were warned to remain indoors for fear of airborne chemical leaks after some complained of respiratory irritations.
City and company officials kept the warnings in place even after the fire was extinguished on Monday evening, as gases were still leaking from breached pipes at the site.
City authorities gave the all-clear on Tuesday evening, saying then that a possible danger to the population could finally be ruled out.
BASF employs over 100,000 people around the world -- around 36,000 of them in Ludwigshafen -- and had sales of more than 70 billion euros ($76.77 billion) in 2015.
The firm's worst accidents lie many decades in the past, including a 1921 explosion in a Ludwigshafen ammonia factory that killed 585 people and a 1948 accident on the same site in which 207 were killed and 3,800 injured.