The dollar demand was so strong that renewed capital inflows could not stem the rupee fall, dealers said.
At the Interbank Foreign Exchange (Forex) market, the domestic unit opened weak at 49.08/09 a dollar from overnight close of 48.75/76 due to early weakness in equities.
However, a sudden gust of dollar buying by importers, mainly oil refiners, to meet their monthly requirements weighed on the rupee and it fell back to a low of 49.15.
It concluded the day at 48.96/97, a fall of 0.43%. In last two days, it had gained by 70 paise or 1.42%.
The rupee depreciated by almost half per cent on dollar buying by importers despite weak dollar against other major currencies and firm local equities, which closed up by over one and half per cent, Alpari Financial Services (India) CEO Pramit Brahmbhatt said.
The dollar index, consisting of six major currencies, was down by nearly 0.4% and New York crude oil was trading above $81 a barrel in European market on Thursday.
The BSE benchmark Sensex, which was down by about 130 points in late morning deals, bounced back and closed up by over 252 points or 1.53%.
FIIs injected $69.53 million in equities on September 27 and 28, as per Sebi data.
RBI fixed the reference rate for the US dollar at R48.9253 and for the Euro at R66.6458.
The rupee premium for the forward dollar declined on fresh receivings by exporters.