The benchmark oil price slipped further below $58 a barrel on Thursday on concerns about global economic growth, oil demand and signs of excess supply despite Opec-led cuts.
Egypt's blue-chip index declined 1.1% with the country's largest lender Commercial International Bank dipping 0.4%, while EFG Hermes was down 2.6%.
Activity in Egypt's non-oil private sector rose fractionally in September but remained in contraction territory for the second consecutive month, a survey showed on Thursday.
Saudi Arabia's index lost 0.8% with Al Rajhi Bank down 1.1% and Sahara International Petrochemical (Sipchem) plunging 5% as the stock traded ex-dividend.
On Monday, government data showed that Saudi Arabia's economy slowed sharply in the second quarter as the world's largest crude exporter cut oil output, raising fears of an economic contraction this year.
In Qatar, the main share index ended 0.5% lower, driven down by a 1.4% fall in Qatar Islamic Bank and a 0.6% slip in Qatar National Bank.
Qatar's economy contracted by 1.4% in the second quarter compared to a year earlier, hurt by a drop in the manufacturing and construction sectors.
In Abu Dhabi, the index slipped 0.1%, extending losses for a fourth straight session as market heavyweight First Abu Dhabi Bank dropped 0.7%.
"MENA markets are reacting to the weak global lead and falling oil prices. It is interesting to see Dubai holding up better, especially the Emaar names after a bad start to the quarter," said Vrajesh Bhandari, senior portfolio manager at Al Mal Capital.
"Historically, the fourth quarter has been generally a negative one for UAE markets - explained by local institutions wanting to book profits and come back in the new year with fresh capital allocations prior to the dividend season."
He added that the market mantra is to selectively pick stocks as there were not many broad themes. With third quarter results set to begin this will allow a fresh look at the underlying fundamentals and the industry landscape.
In Dubai, the index rose 0.6%, led by real estate stocks. Blue-chip developer Emaar Properties increased 2.3%, while its unit Emaar Malls was up 2.2%.