The hosts were without their big centre-back, Peter Jang, who suffered a muscle tear last weekend at Lobi Stars.
Cameroon defender, Saidou Moussa, filled in centre-back in Jang's absence in his first game in front of the home fans after his debut against Lobi Stars.
Five-time league champions, Heartland still without their influential captain, Chinedu Efugh since the start of the season soldiered on to a fine start.
Attacking winger, Bright Ejike, put the Naze Millionaires in front after 19 minutes inside the Pantami Stadium in Gombe.
Heartland held on to their lead into the break but were made to pay for sitting too deep in their half just 11 minutes into the restart when Suleman Usman equalised for the hosts.
The contest continued with both teams tied on 1-1 but it was Adamu Mohammed's strike inside the last 10 minutes that proved decisive for the Scorpions to pick their first full points of the season.
Maurice Cooreman expressed delight at guiding his men to their first full points of the season and praised his team for the result.
"It is a good result for us today. The boys did well to come back and win the match. Now we will work to build on this result as we have been playing well in our past games but we've not been lucky to win," Cooreman told Naijaligue.blogspot.com after the game on Friday.
The win lifts Gombe United from bottom spot to eighth position while Heartland drop from 14th to 15th position in the NPFL standings.