Ghanaian-born striker Joetex Frimpong of El-Kanemi emerged as the Nigerian league's top scorer with 18 goals, three more than Victor Ezeji from Sharks.
However, the champions had to come from a goal down to beat El-Kanemi, who needed a win to steer clear of relegation.
David Takyase opened scoring for El-Kanemi early in the match before former youth international John Ofomba netted the equaliser from the penalty spot five minutes from the break.
Striker Eric Fascindo ensured the team known as 'The People's Elephant' keep the crown they first won July last year when he scrambled home the match-winner in the second-half.
Enyimba, from the Eastern Nigeria city of Aba, finished their campaign on 61 points from 34 matches.
Aba was thrown into a big party as jubilant fans sang and danced in praise of the champions, who were presented with their trophy by top officials of the Nigeria Football Association (NFA).
"It was a well deserved victory. We really worked hard for it," said club boss Felix Anyansi.
The newly-crowned champions will again represent the country in the African Champions Cup next year.
They were knocked out of this year's Champions Cup in the second round by Asec Abidjan of Ivory Coast, but Anyansi predicted his team will go all the way to the continent's top prize next year.
"We lost to Asec because of inexperience. But we have learnt our lessons from our elimination and I promise we will do very well in the coming year," he said.
Enugu Rangers defeated bottom team Jasper United 3-1 to finish as runners-up with 57 points and will feature in the CAF Cup next year.
Four teams - NPA, Yobe Stars, El-Kanemi and Jasper - were relegated to the lower division while Kwara United, Dolphin, Delta United and Niger Tornadoes were promoted to the top flight.
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