Qatar's index fell after MSCI again kept the gas exporter as a frontier market, saying foreign ownership limits prevent it from being rated as an emerging market.
Doha's benchmark fell 0.6 percent to 8,724 points, trimming 2011 gains to 0.4 percent.
Qatar National Bank fell 0.8 percent, Industries Qatar shed 0.7 percent and Commercial Bank of Qatar was down 1.1 percent.
MSCI warned in June that Qatar's 25 percent foreign ownership limit would stop it being upgraded. The stock exchange has asked companies to raise limits.
"Qatar didn't make enough progress in opening up some of the higher profile stocks to foreign investors to the extent that these investors would like," said Ibrahim Masood, senior investment officer at Mashreq Bank in Dubai.
"There's clear interest from foreign investors in Qatar getting emerging market status."
UAE markets fell after index compiler MSCI denied an upgrade to emerging market status, citing concerns over effectiveness of a new delivery-versus-payment settlement systems.
Dubai's index fell 1.6 percent to 1,363 points and Abu Dhabi's benchmark declined 0.6 percent to 2,427 points.
Emaar Properties, which had risen in the run up to the decision, dropped 4.3 percent, Dubai Financial Market shed 3.2 percent and Drake & Scull dipped 2.5 percent.
Abu Dhabi stocks also declined, with Aldar Properties down 4.2 percent and Dana Gas falling 1.9 percent.
UAE's two main bourses implemented DvP in 2011 and MSCI said it received "very positive" investor feedback since the implementation, but concerns remain.
"We were expecting the reason behind the UAE decision to be related to low volumes and not the dual account structure," CAPM Investment says in a note. "We hold the view that the new DvP model (as well as its failed trade processes) has been well tested, and the real reason behind the international investors' concerns and the MSCI decision is the lack of volume."
Turnover on Dubai's index in 2011 is about a tenth of 2008 and at its lowest level for at least seven years.