"Alex De Angelis, who does not remember because of the head injury dynamics of his accident, will be transferred to Italy during the next week," the team said after the rider had undergone a CAT scan.
Ioda added de Angelis had not suffered any spinal cord injury.
The rider crashed midway through FP4 leading to the session being red-flagged at the Motegi circuit and was taken by helicopter to the Dokkyo Hospital in Mibu.
No television footage of the incident was shown, with de Angelis riding one of the least competitive bikes on the grid and having only scored two points this year following a spate of retirements.
The incident led to a delay in a breathless qualifying session where Lorenzo edged Yamaha team mate Rossi to take pole position by just 0.081 seconds.
Lorenzo trails Rossi by 14 points in the championship with only four races to go this season but looks set to cut that deficit on a track he has shown his fondness for by coming out top in all the sessions this week.
The Spaniard used a two-stop strategy, after some front end issues on his first run, to record a best time of 1 min 43.790 seconds to deny the Italian, who had gone top moments before with his best lap.
It was Lorenzo's fourth pole of the year and Yamaha's first one-two qualifying performance of the season.
"I made the maximum and it is a good lap time," double MotoGP champion Lorenzo told reporters.
Rossi, bidding for his seventh MotoGP world title, was optimistic he could better Lorenzo come race day.
"I was confident for the qualifying. I did a good strategy (and) I was in the right place. I am very positive looking forward for tomorrow. I can be competitive with Jorge," he said.
Defending champion Marc Marquez was third for Honda in 1:44.216 to round out the front row.
The Ducati duo of Andrea Dovizioso and Andrea Iannone finished fourth and fifth for Sunday's race with Marquez's Honda team mate Dani Pedrosa completing the second row.
(Writing by Patrick Johnston in Singapore; editing by Amlan Chakraborty)
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