Deuba received 139 votes against his opponent Paudel's 67. The party has 207 members in the Parliament.
Total 206 votes were cast and none was declared invalid as the party had used electronic voting machine, the Himalayan Times reported.
Three-time prime minister, 69-year-old Deuba was elected as the president of the Nepali Congress during the party's 13th general convention in Kathmandu last month.
The post was vacant since February 9 when the then party President and parliamentary party leader 79-year-old Sushil Koirala died.
"This election is the internal democratic exercise of the party," Deuba told reporters. "There is no win and loss, it is the question of only who got what responsibility."
"We got to work towards making the country prosperous and strengthening the federal democratic republic. I will dedicate myself to this as far as my capacity," he added.
Deuba is 8th president of the party since its inception. He was the prime minister of Nepal from 1995 to 1997, from 2001 to 2002, and from 2004 to 2005.
He will be an ex-officio member of the Constitutional Council as the chief of the opposition in the Parliament.
