The Italian beat Vicente Reynes (Lotto-Belisol) to the line in a bunch sprint at the end of a 112km stage in the capital of Cameroon, Yaounde.
The 23-year-old Palini, who was third in the opening stage, takes the overall race lead from Monday’s stage winner Frederique Robert.
"This is a very important victory for me since it's so important to start the new experience in the team in a winning way," Palini commented.
"I also appreciate the joy of a victory in such an unconventional cycling atmosphere."
The eighth edition of Africa's only 2.1 rated race by the UCI sees nine African national teams join UCI ProTeams Lampre-Merida and Lotto-Belisol plus Europcar, Cofidis, Groupement Sportif Oil and MTN-Qhubeka in the seven-day race.
Janse Van Rensburg (MTN-Qhubeka) and Abdelmalek Madani (Groupement Sportif Oil) escaped early and opened up a 5:30 lead after 50km..
But Lotto-Belisol and Lampre-Merida did some hard chasing and the duo were caught with 8km remaining to set up the bunch gallop to the line.
French duo Adrien Petit (Cofidis) and Yohann Gene (Europcar) plus Eritrea's Meron Amanuel completed the top five.