Rodriguez, who won Lombardia in 2012 and 2013, injured his right knee on training on Friday and will not start in the final WorldTour race of the season.
"Yesterday morning, before leaving for Italy, I was doing a last training behind a motorbike. Just when I dropped from the motorbike, I did not notice a traffic sign post and hit it with my right knee. I did not crash but immediately I felt a lot of pain," Rodriguez said.
"Fortunately I was not far away from home and I managed to arrive home by bike. In the evening, after my arrival in Italy, the pain was getting worse.
"My knee was swollen. It was even getting hard for me to walk. It is just impossible to race now. This is a real bummer. I was really motivated for this race."
Later tests revealed a hematoma inside the right knee and Rodriguez immediately returned to Spain where an MRI will be performed to exclude further damage.
This is sad news for Joaquim and for the team, team director José Azevedo said. After the Vuelta a España, where he finished second, Joaquim kept on training for Il Lombardia, his last big goal of the season.
"Also for Team Katusha this is an important race as we are still fighting for the number one position in the UCI ranking. We still have Dani Moreno and Ilnur Zakarin. We will fight for it, but we will miss Joaquim."
Rodriguez will be replaced in the line-up by Jacopo Guarnieri.