At the closing bell, the BSE gauge Sensex was down 38.88 per cent or 0.09 per cent at 41,642.66; while the NSE barometer Nifty was lower by 9.05 points or 0.074 per cent at 12,262.75.
Index heavyweight Reliance Industries, which slipped 1.78 per cent on the Sensex, was a top drag after the government sought to block the company's plan to sell stake to Saudi Aramco.
In percentage terms, Nestle India was the top loser in the Sensex pack, shedding 2.20 per cent, on its first day as part of the index.
Other major laggards were SBI, Tech Mahindra, ITC and Mahindra and Mahindra.
On the other hand, gains in Maruti, Hero MotoCorp, Kotak Bank, Bajaj Auto and Bajaj Finance restricted the losses on the index.
Traders said the Sensex reshuffle led to some price movements as fund managers adjusted their portfolios.
Yes Bank, Vedanta, Tata Motors and Tata Motors DVR have exited the index to make way for Titan Company, UltraTech Cement and Nestle India.
Sectorally, BSE energy, realty, FMCG, power and utilities indices fell up to 1.33 per cent.
While BSE auto, teck, IT and consumer durables indices rose up to 0.50 per cent.
In the broader market, BSE midcap and smallcap indices too ended up to 0.09 per cent lower.
Subdued trading in global markets ahead of year-end holidays and a disappointing show by the ruling BJP in Jharkhand polls also made investors cautious on the domestic bourses.
"Even though the markets closed almost unchanged from previous close, both the indices exhibited sideways movement and ended marginally lower. Auto stocks overcame the weak sentiment with Maruti, HeroMoto Corp logging gains while HDFC twins leading the uptick among the financials. Disappointing political verdict also prompted investors to cut their positions after BJP failed to win the majority in Jharkhand...," Shrikant Chouhan, Senior Vice President, Equity Technical Research, Kotak Securities, said.
Auto stocks traded positive ahead of fresh launches due next month while banking stocks witnessed a profit-booking.
Analysts also said that investors remained on the sidelines in absence of fresh triggers in a holiday shortened week.
There is a growing confidence among investors that the government will address the growth concerns through adequate measures to boost consumption and investment to maintain the buoyancy in the market, they said.
In global markets, bourses in Shanghai and Seoul ended on a negative note, while those in Hong Kong and Tokyo settled in the green.
Europe was trading on a tepid note in early deals.
On the currency front, the rupee depreciated 6 paise to 71.16 against the US dollar.
Brent futures, the global oil benchmark, slipped 0.05 per cent to USD 66.11 per barrel. ANS MKJ