Malik, 24, has been reported twice by match officials in the last two years and has primarily played as a batsman. The operation took place in Cape Town, removing floating bones from his right elbow and repairing tissues.
He has been advised to rest for six to eight weeks before batting and bowling again.
''I suffered pain in my right elbow while batting or bowling and it was one of the reasons why I had problems extending it properly,'' Malik told Reuters yesterday.
''I am happy that this problem is done with now.
''I am confident I will be fit by the time the team leaves for England in late June. It is a tour I have been looking forward too for a long time,'' he said.
Malik said his elbow had been damaged in a road accident in 2003 and due to his cricket commitments he could not take time out to get it repaired. He has played 15 Tests and 117 One-day internationals.
Fast bowler Shoaib Akhtar has started bowling again after a knee operation in Australia earlier this year.