The spillover from a weak global market also cast its shadow.
Caution prevailed in a choppy trade ahead of the US Federal Reserve meeting next week and worries over Britain's referendum on its European Union membership on June 23, which dented sentiment.
Both the indices have recorded their first fall in three weeks.
After opening lower, the 30-share Sensex staged a strong comeback on value-buying coupled with short-covering but closed the day lower by 127.71 points, or 0.48 per cent, at 26,635.75.
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The wider NSE Nifty closed a shade lower than the 8,200-mark at 8,170.05, down 33.55 points, or 0.41 per cent, after shuttling between 8,162.85 and 8,265.60.
Realty, auto, PSU, consumer durables, oil and gas, technology, IT, banking, FMCG, capital goods, metal and healthcare stocks melted.
The PSU banking index on NSE lost more than 1.5 per cent after Moody's Investors Service said weak earnings outlook for PSBs raises concern over high level of external capital need and their capitalisation profile is expected to deteriorate unless the government offers additional support.
"Today marked the third consecutive day of losses, with the Sensex and the Nifty closing lower by nearly 0.5 per cent. Markets traded volatile as participants remained indecisive about the immediate future direction of the indices," said Shreyash Devalkar, Fund Manager - Equities, BNP Paribas.
Brokers said lacklustre Asian shares and a lower opening in Europe on growing concerns about outlook for the global economy clouded sentiment.
Japan's Nikkei fell 0.40 per cent and Hong Kong's Hang Seng index shed 1.20 per cent while China's financial markets were closed for a public holiday.
Others that faltered included Tata Motors, Coal India, SBI, Maruti Suzuki, ONGC, Asian Paint, ITC, Cipla, ICICI Bank, TCS, HDFC, Infosys, L&T, Bajaj Auto, Hero MotoCorp and Dr Reddy's, falling by up to 2.04 per cent.
Sector-wise, realty burnt its fingers the most by falling 1.03 per cent, followed by auto, PSU and consumer durables.
In line with the overall trend, broader markets too remained feeble, with the mid-cap index falling 0.40 per cent and small-cap 0.20 per cent.
while ONGC ended steady.
Major losers included RIL 2.63 per cent, Hero MotoCorp 2.56 per cent, ICICI Bank 2.47 per cent, M&M 2.21 per cent, Maruti 2.04 per cent, Tata Motors 2.02, Cipla 1.98 per cent, HDFC Bank 1.94 per cent, Asian Paints 1.51 per cent, Wipro 1.46 per cent, Tata Steel 1.41 per cent, Sun Pharma 1.38 per cent and SBI 1.32 per cent.
Among the smart mover were TCS 0.88 per cent and Coal India 0.31 per cent.
Among BSE sectoral indices, oil&gas tumbled 2.19 per cent followed by energy 2.04 per cent, auto 1.93 per cent, healthcare 1.70 per cent, power 1.56 per cent, consumer durables 1.55 per cent, utilities 1.42 per cent, bankex 1.36 per cent and telecom 1.31 per cent.
The market breadth remained negative as 1,895 stocks closed in the red, while 835 stocks finished in green and 135 ruled steady.
The total turnover fell to Rs 3,320.99 crore from Rs 3,531.69 crs yesterday.