A motorist was hit by one of the rocks at around 10pm on Tuesday, police in the German city of Flensburg confirmed to TV Syd.
The bridge in that incident is just south of the frontier between the two countries at Padborg, according to the report.
Police, fire services and medical response personnel all attended the scene, where a granite rock smashed through a car windscreen, injuring a 58-year-old woman.
The woman, who is Danish, reportedly lives in Flensburg but works in Denmark.
She was seriously injured and was admitted to hospital in the German town, according to TV Syd.
Her car was hit on the German A7 road near Ellund, just south of the E45 motorway near Padborg. A granite rock measuring approximately 25×25 centimetres was subsequently found in the central reservation as the police clear-up operation caused a 300-metre traffic tailback on the southbound carriageway on the Danish side of the border.
No arrests have yet been made.
Around half an hour prior to the incident, a rock was thrown from another bridge in the area near Brarup, around ten kilometres further south in the German province of Schleswig-Holstein. No injuries occurred in that incident, German police confirmed to TV Syd.
Similar incidents involving the throwing of rocks from bridges onto motorway traffic have occurred repeatedly near Odense, Denmarks third-largest city.
A concrete block was thrown from a bridge in 2016, killing a German woman who was travelling in a car on the E20 motorway near the city.
In September 2017, a rock weighing 40 kilograms was thrown from a second bridge, around 200 metres from the site of the first crime. Nobody was injured.
In December, police in Odense described as serial criminals the person or persons behind the acts.