The 17-year-old was unleashed by coach Carl Veart in the 76th minute on Friday night with Adelaide leading the visitors 3-2 and the game in the balance.
With five minutes of normal time to play, Isaias won possession in the middle of the park and lofted a perfectly weighted pass over the City defence for Irankunda to race on to.
The speedster flew past his opponent Curtis Good, took a touch and fired into the top corner past the onrushing Tom Glover, sealing the win for United.
The goal was Irankunda's third for the season, and second in as many matches following his stunning 87th minute equaliser against Melbourne Victory last week.
It came four weeks after he'd clinched maximum points with an 82nd minute rocket in a 2-1 triumph over Brisbane Roar.
"He's 17 – it takes years to build up the work that you need to play at this level, and just not the physical aspects," said Veart.
"It's the tactical aspects as well and he's starting to understand that and his role in playing those positions.
"I know I've said this many a time - I think the top is easily attainable for him.
"If he keeps working, if he keeps his head switched on and has good people around him, giving him good advice and he listens to the right people, he will go all the way to the top."
The Reds found themselves behind on nine minutes after Andrew Nabbout gave the visitors the lead.
United equalised in first-half stoppage time before two goals early in the second half had Adelaide in pole position on the hour.
City made it 3-2 soon after and enjoyed a brief spell, before Irankunda snuffed out any hopes the visitors had of salvaging a point.
"We're a very good side at home," Veart said.
"We've shown that this year and we've shown again tonight that at home we're a very difficult side to play against."
Melbourne City coach Rado Vidosic acknowledged City slipped away in the second half after dominant periods in the opening 45 minutes.
"The second half, we just started to give the ball away, take some unnecessary risks, we were not clean in our passing and in our controlling," he said.
"That is where we failed, in those moments where we should've kept the ball a little bit better and definitely for longer periods of time."
