The activists said the compound was run by the Political Security Department, one of Syria's four most powerful intelligence agencies.
Amateur videos showed rebels raising an Islamic flag on top of the three-story building as fighters carted away rifles and boxes of ammunition.
Deir el-Zour has been the scene of heavy fighting since the uprising against Assad began in March 2011. The province, which goes by the same name as the city, is located along Syria's border with Iraq and includes several oil installations that the rebels have repeatedly targeted.
The aid group Doctors Without Borders said last month that government forces are shelling and bombing Deir el-Zour almost daily. It said tens of thousands of Syrians, many of them wounded, remain trapped in the city.
Also Tuesday, regime warplanes also carried several airstrikes on rebel positions in restive towns and villages around Damascus, including eastern Ghouta and Yalda, the Observatory said. The group relies on reports from activists on the ground.
After capturing several major army bases and government outposts, the rebels control large swathes of land in northeastern Syria. Assad's troops, however, continue to hold a tight grip on the capital after nearly two years of conflict.
The areas on the capital's doorstep have been rebel strongholds since early on in the revolt. In recent months, the rebels have used them as a base from which they have been trying to push into central Damascus, the seat of Assad's power.
Back on the front line in Aleppo, a veiled female sniper who identified herself as Givara told the AP that when she decided to fight against Assad's troops people used to tell her that it would be difficult as a woman.
"No it's not difficult ... I want to defend my life," she said, adding that her husband is proud of her and that she was fighting because she didn't want to see her children reduced to "pieces of flesh" by government attacks.
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