The teen sensation was performing in front of thousands of fans on the third night of the London leg of his world-wide tour when he fell ill.
His manager Scooter Braun said he was seen by a doctor backstage at the venue who told him not to return to the stage.
However, fans reported that he did make it back to the spotlight to finish his Believe show.
In a video posted by a fan on YouTube, Bieber's manager Scooter Braun tells the audience: "Justin got very light of breath, the whole show he's been complaining. He's backstage with the EMTs (emergency medical team) and the doctor.
"They're telling him they want him to go and see somebody and find out what's going on with his lungs, he's just told me that in five minutes, if it's OK with you guys, he's going to come out and finish the show.
"So he might not be jumping around as much and everything else, you guys need to be patient with us, we're not trying to be disrespectful, we're not trying to get you guys home late, we're truly trying to put on a show for the people who love him."
The manager had previously tweeted his joy that Bieber started the show 10 minutes early.
One fan tweeted: "Biebers not well and has gone off stage!
"He literally was so out of breath on stage in the middle of beauty and a beat and then went off!"
She later added: "Aww @justinbieber came back in stage after the doctors told him not to and he was incredible #believe #inspiration."
Bieber then published a picture of himself in a hospital bed after being checked by doctors for breathing problems.
The singer, who uploaded the pictures to his Instagram account, also thanked fans for supporting him while he "figures out" what happened.
He said: "Getting better. thanks for everyone pulling me thru tonight. best fans in the world. figuring out what happened. thanks for the love."
But fans raised questions over the timing of his illness, claiming it is a publicity stunt to win back their affection after he was slammed for his late appearance on Monday night.
On fan claimed on Twitter: "Justin Bieber was not sick, its a Publicity Stunt to make up for his late show."
While another speculated: "Justin Bieber publicity stunt collapse because he cocked up the other night by being 2 hrs late for his fans. Anything for sympathy?"
The singer was heavily criticised by fans and parents of young children for starting his concert late on Monday night.
Many were reduced to tears when forced to leave the venue just minutes into his performance, which started shortly after 10pm, in order to catch trains homes.
Bieber later apologised and blamed the delay on technical difficulties.
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