The Jakarta Composite Index (JCI) plunged 2.3 percent or 110.9 points to 4,763.37 at the close of the first session, while the rupiah slumped by 1.7 percent ( 234 points ) to 13,428 per US dollar.
"Series of quick-count results showed that the close victory of Brexit has squeezed the pound sterling and several currencies in Asia, including the rupiah," said Monex Investindo Futures head of research Ariston Tjendra as quoted by Antara news agency in Jakarta on Friday.
The surprising result, he further said, had driven global investors to divert their assets from the risky instruments to the safe haven, including the US dollar.
As of 1 p.m, Brexit supporters led the tally with 51.9 percent votes. Victory for the "Leave UE" campaign fans speculation that more countries could withdraw from the EU amid the fragile recovery of the world economy.
Indonesia Stock Exchange (IDX) data showed 245 stocks declined and only 38 stocks increased. Another 247 stocks remained unchanged. All nine sectoral indexes retreated, with the Miscellaneous Industry Index leading the correction with a 4.83 percent drop, followed by Basic Industry Index ( 2.82 percent ) and Agriculture Index ( 2.79 percent ).