Germany international Khedira, who joined Real from VfB Stuttgart in 2010, will leave Real for free at the end of the season, with Chelsea, Manchester United, Arsenal and Liverpool, as well as Juventus, reportedly keen to sign him.
The 28-year-old has barely featured since the turn of the year, with Real citing a series of minor injuries as the reason for his absence, but Khedira told sports daily Marca the club had decided he was no longer wanted.
"I did have a small injury, a pain in my right heel, but that wasn't why I wasn't playing," Khedira said in an interview published in Saturday's edition of the newspaper.
"It wasn't a complicated injury, I was able to play," he added.
"I've always felt that I've had the coach's backing, but the message indirectly came through to me that I was no longer needed, I was frozen out and wouldn't have a chance to continue playing.
"It's not the end that I wanted. It hurts that I'm accused of a lack of professionalism because I've always put the team ahead of myself. I've always gone with the truth."
Khedira is not in the squad for Real's final La Liga match of the season at home to Getafe later on Saturday.
"Nobody from the club said anything to me directly," he told Marca. "It's all feelings, incidents and comments saying I wouldn't play any more. But nobody approached me.
"What has happened this season has hurt me to the bottom of my soul."
Khedira posted a farewell message on his Instagram account on Saturday after his final visit to Real's Valdebebas training ground.
"Valdebebas for the last time," he wrote. "I am moving on but I will surely miss my club Real, all of its staff and my unbelievable team mates! Guys, it was one heck of a ride!!!"
Real will end the campaign without a major trophy after failing to defend their Champions League crown and trailing Barcelona who wrapped up the La Liga title last weekend.
Carlo Ancelotti's side were knocked out in the last 16 of the King's Cup by Atletico Madrid in January.
(Reporting by Iain Rogers, editing by Ken Ferris and Toby Davis)
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