Factional fighting overshadowed a week of closed-door talks at the five-yearly Communist Party Congress. But Trong, 72, retained his position as his rival, reformist Prime Minister Nguyen Tan Dung, was pushed from power.
Dung remains prime minister but will step down later this year when the National Assembly convenes to appoint a replacement. This is expected to be Nguyen Xuan Phuc, currently a deputy prime minister, state media said.
"Delegates to the first meeting of the party's central committee congratulated Comrade Nguyen Phu Trong who was elected general secretary," the official Vietnam News Agency reported.
Dung, 66, a two-term prime minister and political heavyweight, is credited with pushing a pro-business agenda and talking tough to China over a festering maritime dispute.
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He had been tipped to ascend to the party leader position but in the end he lost out in internal elections. He was not selected for the 180-member central committee, which in effect ends his official political career.
Although both his reformist credentials and achievements in office were debatable, he was unquestionably "someone who had a vision", said London, adding his exit marked a return to a more moderated style of governance.
"The (Communist) Party has been around for 85 years and always been steered by committee -- in this context, the 'go slow' approach makes sense," he added.
Trong's ascent -- which owes more to Dung's divisiveness as to his own popularity -- is unlikely to mark a dramatic change of course on key issues such as a dispute with Beijing over parts of the South China Sea and participation in a series of trade deals, including the US-led Trans Pacific Partnership.