Ivanovsky was born in Gdov, Russia, and studied natural sciences at St. Petersburg University, graduating in 1888. He obtained his master's degree in botany in 1895 and worked (1896–1901) as an instructor in plant anatomy and physiology at the Technological Institute, St. Petersburg. In 1908 he was appointed professor at the University of Warsaw.

In 1892, following his investigations of tobacco mosaic disease in the Crimea, he demonstrated that a filtrate of the sap from infected tobacco plants had the ability to transmit the disease to healthy plants. Ivanovsky showed that minute crystalline particles were present in the filtrate and asserted that they were somehow linked to the disease. However, he wrongly attributed the cause of the disease to minute bacteria. Ivanovsky's work was confirmed in a publication by the Dutch bacteriologist Martinus Beijerinck in 1898. It was Beijerinck who stated that such infective agents are not bacterial and coined the term virus. This, together with the work of the French bacteriologist Charles Chamberland on rabies, was one of the earliest pieces of evidence for the existence of viruses although it was not until 1935 that Wendell Stanley confirmed this.