The driver was found dead on Monday evening, while the body of her passenger was found on Tuesday morning further downstream.
A third woman died in the town of Hechingen after rising water trapped her in her basement.
Meanwhile, a train engineer was seriously injured near Sigmaringen when the regional train he was driving hit trees that had been blown onto the tracks by heavy winds.
He was taken by helicopter to a military hospital in nearby Ulm.
The storm, which began on Monday at around 1730 GMT, also caused considerable delays at the nearby Stuttgart airport and millions of dollars in damage.
Maute said: "The vehicles are standing all over the place, in the craziest positions."