Police in the northern city of Rostock said the animal disrupted traffic, damaged cars and caused an accident on the A20 motorway on Wednesday before being shot dead by officers.
A second zebra that escaped from the circus was captured.
Details of the shooting have not been made public.
It is also not yet clear how the two animals escaped from the circus in northern Germany on Tuesday evening.
Police on Wednesday morning issued a warning on Twitter that one of the escaped zebras was disrupting traffic on the A20 highway and had caused an accident.
"The animal was going in the wrong direction on the autobahn from Tessin to Rostock," a police spokesperson told Deutsche Welle.
In a later statement, they said no one was injured in the collision, which occurred when one car braked to avoid the animal, causing another to crash into it.
The animal also damaged vehicles and forced the temporary closure of the highway, they said.
The zebra was later shot near the municipality of Thelkow after efforts by officials and a circus tamer to capture it alive were unsuccessful.
The second zebra was reportedly returned to the circus. BBC