The EIA said crude oil stockpiles dropped by 9.9 million barrels in the week to 373.9 million.
Stocks remain near the upper limit of the average range for this time of year, but supplies dropped more than expected and the decline, along with geopolitical tension in Egypt, combined to send oil prices higher.
West Texas Intermediate crude closed at $106.52 per barrel on the New York Mercantile Exchange, although prices shed 35 cents in afterhours trading to $106.17 per barrel.
Reformulated blendstock gasoline in after hours trading shed 1.81 cents to $2.9968 per gallon. Home heating oil lost 0.47 cents to reach $2.997 per gallon.
Natural gas gave up 1.4 cents to $3.666 per million British thermal units.
At the pump, the average price for a gallon of unleaded regular gasoline was $3.501, up from Tuesday's $3.483, the AAA Fuel Gauge report said.