The Caf Champions League took the centre stage on Friday as Group C matches got underway in the afternoon.
As they were sitting third before this match but separated by goal difference with Mamelodi Sundowns ahead of the tie, Horoya were looking for a win at home.
As early as the 11th minute, Ocansey Mandela found the back of the net for the hosts to put them ahead.
Mandela's strike helped the hosts to remain ahead at the interval, but they allowed the visitors to level the matters in the second half.
Ablamvi Ayi Djadja equalised in the 51st minute, but their celebrations were shortlived as Horoya regained their lead through Bolaji Simeon Sakin, who doubled their lead in the 59th minute.
The victory for Horoya saw them leapfrog Sundowns to go second on the log with eight points from five matches.
However, they will hope to collect maximum points when they meet Pitso Mosimane's men in their final match next week in South Africa.
In the second match of the day, log leaders Wydad Casablanca faced Sundowns in the second match of the day.
The defending champions welcomed the 2016 champions at Stade Mohammed V at 21:00 in Morocco following a 1-1 draw in Pretoria.
Sundowns were under pressure in the clash chasing their second group win.
On the other hand, a draw would have been a favourable result for the reigning Premier Soccer League (PSL) champions to retain their knockout stage qualification hopes.
It was a tight affair in North Africa as Sundowns contained the hosts, but both camps could not break the deadlock in the opening half.
However, the hosts were not to be denied in the 56th minute as they broke the deadlock through right-back Anas El Asbahi, who unleashed a stunning shot from way out, beating Denis Onyango on his left corner.
The visitors tried to throw bodies upfront after the 70th minute and also protested for a penalty, but it was not to be.
In the last four minutes, substitute Ali Meza received possession in a promising area, but his shot at goal was easily swallowed by Yassine El-Kharroubi.
The victory saw the North Africans win the group with a game to spare having collected 11 points from five matches already while the South African champions slipped to third on the table.