Qatar's Union Development Company (UDC) slumped a day after it said it is in talks to issue shares to a state pension fund worth QR160m ($43m).
Shares in the developer, which had been suspended on Wednesday, fell 10 percent to end at a three-week closing low as investors fretted about being diluted.
The stock hit a two-year high on Dec 19, rallying for a few days after the developer said it had initiated talks with a strategic investor.
Qatar's index ended 0.4 percent lower at 8,779 points, its largest one-day decline in about two weeks.
Abu Dhabi real estate stocks closed on sharp gains after the government bailed out Aldar Properties with a AED16.8bn ($4.57bn) lifeline the previous evening.
Aldar ended at a two-week closing high, up 9.5 percent.
The government bought some Aldar assets, retired a loan and lent it money to complete its Capital Market project.
Peer Sorouh Real Estate also jumped up 7.6 percent. The main index climbed 1.5 to 2,402 points, up for a second session running.
Neighbouring Dubai's benchmark rose 0.5 percent to close at 1,353 points, extending December losses to 1.9 percent.
Markets in Oman and Kuwait ended higher in the final trading day of the year but the two indices ended deep in the red in a tough year for equity markets.
Oman's index rose 0.3 percent to 5,696 points. For the year, it closed down 15.7 percent.
Heavyweight Bank Muscat gained 0.5 percent, Oman Cement climbed 2.4 percent and Ahli Bank rose 1.1 percent.
"The [Omani] market is led by conviction from local institutional buying in index heavyweights looking at the medium-term horizon," said Kanaga Sundar, head of research at Gulf Baader Capital Markets in Muscat. "Positive buildup in the markets may be seen during the coming weeks on earnings and dividend expectations."
Oman climbed 5.1 percent in December, mostly on expectations of high-yield dividends. But that was not enough to erase yearly losses.
The market fell to a two-year low in the summer, tracking a tumble in global shares amid debt woes in Europe and United States.
Bluechip Renaissance Services was hit in August, dragging the index lower, after it reported serious financial fraud at unit Topaz and reported a 77-percent drop in first-half net profit.
Its shares ended flat on Thursday, having lost 51.4 percent in 2011.
In Kuwait, the index ended 0.4 percent higher at 5,814 points, and down 16.4 percent on the year.
Insurance stocks spiked in year-end trade, an anticipated move in Kuwait as traders tried to boost portfolios for the year.
The market slumped to a seven-year low in August, partly on concerns about local market regulations and lower-than-expected corporate results.
Sentiment was hit later in the year in Kuwait as protests over corruption erupted and eventually led to dissolution of the parliament. The ruler said parliamentary elections will be held on Feb 2.
Trading volumes in Kuwait have been thin in recent weeks, with investors waiting for cues on new political direction.