The German set a time of 10:25 for the out and back 9.2km course along the San Bendetto del Tronto seafront, beating Adriano Malori (Lampre-Merida) by six seconds and Andrey Amador (Movistar) by 10 seconds. Fabian Cancellara (Radioshack-Leopard) was fourth at 12 seconds, despite being in the breakaway during Monday's tough stage in the hills.
Martin powered Omega Pharma-Quick Step to victory in the opening team time trial. He has already won the time trial and the overall classification at the Volta ao Algarve.
"It was more like a prologue than a time trial, and I prefer longer events up to 30/40/50km long. This route wasn't too technical and we were lucky with the weather," he said.
"I expected to fight with Cancellara but in the end it was a fight with Malori. I'm happy after not being able to follow the best in the mountain stages. My form is good, and that's good for the rest of the season."
Martin finished 27th overall, 17:49 behind winner Vincenzo Nibali (Astana). He lost six minutes on the mountain finish to Prati di Tivo and seems to have given up on being a major stage race contender.
"My big goal this season is the world championships," he said.
"I've got a chance to win for a third time in a row and so that's a big goal for me. There's also the team time trial in the Tour de France and the long time trial. I think I've got a good chance there too. We had a super first stage and a good last stage here, so I'm optimistic for the future."