The Israel Start-Up Nation rider was caught in a fall on stage two as the peloton surged towards the Col de la Porte, as Martin immediately realised he was hurt in the fall despite suffering no visible damage.
After riding to the finish, Martin went for medical checks and discovered a fracture in his lower back.
The 33-year-old said: “I was preparing myself for the last climb, for the last effort, and the guys crashed in front of me. I tried to stop in time. One of the guys hit a sign in the road. Immediately I knew I’d hurt myself.
“It’s the weirdest feeling because I don’t have a scratch on me. I just landed full force on the bottom of my bike and unfortunately I have a small fracture down there, a small fracture in my sacrum.”
The crash happened on the valley roads before the final climb when EF Pro Cycling rider Sergio Higuita hit some road furniture and went down.
Martin was unable to avoid the collision and fell hard on his lower back.
Both riders were able to finish the stage, which was hit by a huge hailstorm which sent riders searching for cover.
Martin suffered a non-dislocated sacral fracture and did not start stage three.
He will return home to recover, saying: “I rode to the finish. I could pedal no problem. It was painful and I could tell there was something not quite right. So we went to get checked and we’ve decided not to start day three of the Dauphine. It’s better to go home and recover.
“There’s no reason to be here if I’m not 100 per cent fit.
“Hopefully it heals in time for the Tour.”