The Italian's decision to ride the Tour of Flanders and immediately after start the weeklong stage race in the Basque Country appears to have created the problems. Thursday's time trial further acerbated the now punctured saddle sore.
Nibali will have to rest completely for two days and plans to visit team osteopath, Gianluca Carretta, in the hope of recovering in time for the Ardennes Classics. Nibali is due to lead the Bahrain-Merida team at the Amstel Gold Race, Fleche-Wallonne and Liege-Bastogne-Liege. He will then take time off to prepare for the Tour de France.
Bahrain-Merida team doctor Emilio Magni treated Nibali with antibiotic bandages but that failed to resolve the problem. With the saddle sore now punctured, Nibali was forced to head home early.
"When the bandages came off it was like having my rear waxed," Nibali joked to La Gazzetta dello Sport, playing down the seriousness of his problems.
"My legs hurt and I've got the saddle sore but I've done a good block of work and think an extra couple of days off will do me good. I'll use them to go to see Carretta and get sorted out."
Nibali finished off the pace in the 19km time trial won by Primoz Roglic (LottoNL-Jumbo) and had struggled to be competitive in the hilly road race stages. He won Milan-San Remo but had not raced before lining up at the Tour of Flanders last Sunday. Nibali attacked in the finale of the Belgian Classic and was joined by Niki Terpstra (Quick-Step floors), only for the Dutchman to then drop him and ride to victory.
Nibali caught a plane from Belgium to northern Spain on Sunday night to start the Vuelta al Pais Vasco on Monday but was clearly fatigued in the opening stages dominated by Julian Alaphilippe (Quick-Step Floors).
"We have decided that it was better for Vincenzo to go home because of the importance of the next races in about ten days. It was useless to continue in these conditions and expose the rider to greater risks," Bahrain-Merida directeur sportif Gorazd Stangelj said when the team confirmed Nibali's problems.