The Democratic Republic of the Cong international got his side’s third goal after substitute Frantzdy Pierrot had put the hosts two goals up at Stade de Roudourou.
The Costamoricans came into the game after two winless games against Nancy and Sochaux, respectively.
Pierrot capitalised on Alexandre Vardin's defensive blunder to fire past goalkeeper Jeremy Aymes for his club’s opener on the stroke of half-time.
He completed his brace in the 64th minute before Ngbakoto’s stunner sealed the victory for Sylvain Didot’s men after good work from Mehdi Boudjemaa.
However, the DRC player was replaced in the 87th minute by Mehdi Merghem, while South Africa's Lebogang Phiri and Gabon's Lloyd Palun were on parade from start to finish.
With the win, Guingamp sit in 13th position on the log with 12 points after nine matches, while Le Mans are a place above Paris FC who sit at the base of the table.
They host Rodez in their next league outing on Friday, October 4.
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