The move does not seem to have dented the technology giant's share price, which hit a record high of $115 on Monday.
After Apple, Chinese web services group Baidu was the second most-sold position with four of the top 10 decreasing their positions by a total of $921 million.
Read MoreHedge funds join the Alibaba bandwagon
Ken Griffin's Citadel and Israel Englander's Millennium Management were the top two hedge funds in terms of total equity holdings, followed by Renaissance Management which beat Carl Icahn's Icahn Capital to third spot according to the S&P Capital IQ Hedge Fund Tracker.
Energy and healthcare were the top sector buys thanks to some bumper merger and acquisition deals. Botox maker Allergan, which accepted a $66 billion takeover bid on Monday from Actavis, has been replaced as the top purchase, after the group spent months fending off a hostile bid by activist investor Bill Ackman and Valeant Pharmaceutical.
AbbVie and Actavis are now the most sought-after pharmaceutical groups, with new positions totaling 1.9 billion and $1.5 billion respectively.