The Italian rider crashed and punctured earlier in the stage and, although he didn't lose any more time at the finish, he suggested Giulio Ciccone was now the leader at Trek-Segafredo.
"For now the Giro has been full of suffering," Nibali said after Saturday's stage.
The two-time winner was given the all-clear to start the Giro after his training crash but was still not at 100 per cent, and he lost time at Sestola on stage 4 and on the first summit finish two days later.
On Saturday, he finished safely among the pre-race favourites atop the short climb to Guardia Sanframondi, but revealed it had been anything but a straight forward outing.
"First of all I had a puncture and was forced to change my bike, then when we were going through a town, whose name I don't remember, my bike slipped on a corner out and I fell," he said. "I have some bruises on my body. It was one of those days when if things go wrong, they all go wrong.
"For me, the Giro started uphill and isn't getting much better. That's the way it is right now; I have to deal with it. I will think about recovering and look ahead."
Nibali mentioned Ciccone a number of times, in what could be read as a definitive passing of the leadership baton to his young compatriot.
The signs were already there on stage 4, when Ciccone was given the freedom to move, as he did again in tracking Egan Bernal (Ineos Grenadiers) on the Colle San Giacomo on Thursday. However, whereas the subject was not talked about openly then, Nibali suggested on Saturday that the team will rally around Ciccone.
"Ciccone is going really well," Nibali said. "He has shown he has great legs and a great condition."
In a statement from Trek-Segafredo, he added: "It's right to stay close to him and to support him as a team. Tomorrow will be a tough and important stage. Let's focus on the team goal."
Sunday's stage, the last before the rest day, is a tough short stage with five climbs, culminating with a first-category climb that finishes on steep, gravel roads.
While Nibali is 16th overall, 1:43 down on race leader Attila Valter (Groupama-FDJ), Ciccone is up in seventh at 41 seconds.
"It was a very nervous stage, especially in the first 30 kilometres due to the wind. Unfortunately, Vincenzo first had a puncture and then fell while he was returning. He was unlucky but in the final, he defended himself well," Ciccone said.
"Personally, everything is going well. The last climb was hard but there were no gaps. I think everyone already had tomorrow's tough stage in mind. The sensations remain good, as mentioned in recent days. Every day you have to hold out, there are never really easy days at the Giro, but I can't complain because the condition is good."
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