The on-loan Leicester City forward came off the bench for his fourth league appearance this season and made an impact.
The 23-year-old winger set up Stiven Mendoza to seal the victory in the 90th minute after replacing Juan Otero.
Earlier, Haitam Aleesami had opened the scoring for the Unicorns before Dario Benedetto levelled for the visitors.
Moments before the end of the first-half, Sehrou Guirassy found the net to give Luka Elsner’s men a 2-1 lead.
The win helped the Stade de la Licome outfit climb to 11th spot in the league with 11 points from nine games.
Diabate, who joined the Unicorns in the summer for his second loan spell away from King Power Stadium, has started three games this season.
He will hope his impact against Marseille will help him return to the starting IX when his side take on Nîmes in their next league game on October 19.