"This decision recognises our company's opinion that the safety of Sendai nuclear plant is assured," Kyushu Electric said in a statement.
Shares in the utility jumped after the decision and were 3 percent higher at 0420 GMT.
Local residents who submitted a request to prevent the restart of the Sendai reactors argued the utility and regulator have underestimated the risk from nearby volcanoes and operational plans lacked credible evacuation measures.
A group of disappointed residents gathered outside the court let out a collective sigh when the decision was announced.
Last week it was a different scene in Fukui, where residents cheered after a court slapped an injunction on two reactors at the Takahama station operated by Kansai Electric Power.
The Takahama No. 3 and 4 reactors have cleared the first regulatory hurdles and were expected to restart around November.
"If you compare it to cases before the Fukushima disaster it wouldn't be surprising to see court decisions that are more critical," said Hiroshi Segi, a former judge and an author of books on Japan's judiciary. "That said, those judges remain in a minority."
For Abe, resuming nuclear power - which supplied nearly one-third of Japan's electricity pre-Fukushima - is key to lifting the economy out of two decades of anaemic growth.
The need to import energy has contributed to a trade defecit. Customs data on Wednesday showed Japan's imports of liquefied natural gas at a record-high 7.78 trillion yen ($65 billion) in the fiscal year ended March 31.