The 29-year-old pop star posted a video on Instagram showing lightning flash outside a passenger window while those on board the flight were sat in darkness.
One person can be heard saying "oh my god" as the window was filled with light from the strike.
The craft was finally forced to make an emergency landing due to the "major unexpected storm".
Cyrus posted a photo of what looked like lightning damage to the body of the plane.
No one was hurt in the ordeal, and the Wrecking Ball singer reassured her 163 million followers that she and her crew were safe. However, they were unable to make it to the gig.
One of the largest rock festivals in Paraguay, the Asuncionico festival in the capital of Asuncion is usually held every March at the Espacio Idesa.
Cyrus had been due to perform there along with stars including The Foo Fighters, Machine Gun Kelly and Doja Cat.
The extreme weather conditions led to the second day of performances being totally cancelled by organisers on the grounds of public safety.
Cyrus wrote: "To my fans and everyone worried after hearing about my flight to Asuncion. Our plane was caught in a major unexpected storm and struck by lightning. My crew, band, friends and family who were all traveling with me are safe after an emergency landing. We were unfortunately unable to fly into Paraguay. I LOVE YOU."