Manager Alan Pardew said the former Portsmouth centre-half suffered the fractured in a routine exercise in the club gymnasium and will miss Newcastle's last three games.
Pardew said: 'He was doing a pull-up that went wrong and broke the bone in the top of his arm. He didn't look too clever and we rushed him straight to hospital. He's so unlucky and I feel very sorry for him.
'He has done very well. You get asked a lot of different questions as a centre-half in the Premier League and I've nothing but praise for him.
Ever present: Williamson (right) has featured regularly for Newcastle this season
'His emotions for a centre half are actually quite together because we all know some have a tendency to lose their heads and go through the back of somebody or be a bit more physical but he controls that side of his game well.'
Williamson's absence offers a fresh chance to Steven Taylor, who signed a new contract within weeks of Pardew's arrival at St James's Park but who has started only seven games since due to injury and Williamson's form.
The Newcastle boss said former England Under 21 captain Taylor, who has been tried unsuccessfully at right-back, now had a chance to re-claim the centre-half role.
Pardew added: 'He's in his natural position now. He had a fantastic younger part of his career and then he's hit a bit of a levelling off and that's dangerous for a young player.
Last seen: Williamson (left) played during Newcastle's defeat at Liverpool
'His fitness and injuries have been a big issue and probably one of the reasons why he's flattened out. We've changed his training programmeand his diet a little bit because he was getting big and muscular on top. We've tried to slim him down a little bit and he looks better for that, and he looks quicker.
'He needs to get back moving his career in the right direction. He's ayoung centre-half with tremendous qualities and now he needs to have the mentality to use those.
'He's got the technical ability to play for England but you've got tobe fit every week and have the mentality to work every day.'
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