Heartland head coach, Kelechi Emeteole, made two changes from the team that played Nembe City in mid-week.
Rufus Ebue and Emeka Ogbugh got the nod to start while Kabiru Waziri was named on the bench and Kingsley Ajaero was left out of the match day team.
Enyimba striker, Sibi Gwar was the big name missing from the team sheet of coach Zachary Baraje. The other being goalkeeper Femi Thomas.
Heartland started stronger against their Old Imo Derby rivals knowing that they needed to win their first game of the season.
Inside the opening 10 minutes, Zoumane Doumbia and Julius Ubido got their efforts to strike at goal with the latter's shot forcing Enyimba goalkeeper, Paul Godwin into a save.
The remaining part of the half had little talking point except for the tactical change of Emeteole who opted to send on Benjamin Francis to play in an advanced role as a left-sided midfielder with Doumbia at left-back.
The second half began with Emeteole forced to send on Emmanuel Iwu to replace his first-choice goalkeeper Ebele Obi, who complained of feeling dizzy at the break.
Baraje sent on Ayo Saka and Cameroonian striker Rafael Boumsong to replace Kingsley Sokari and Abdulrahman Bashir respectively in a bid to force the result to sway in Enyimba's favour.
But it was Badarou who scored a half volley on the turn with a minute before time to ensure that Heartland end their hoodoo of more than two years of failing to win against Enyimba in the Old Imo Derby.
It was Badarou's third goal in four matches since he was snapped up by Heartland this season.
The win ensures the Owerri club climb out of the bottom-four until Sunday when eight other matches hold in the Glo Premier League.