Riyad Mahrez's free kick — through a wall that jumped early and left an inviting gap for the Algeria winger — put the visitors ahead in the 71st.
Both teams will now lock horns on May 5 in the second-leg semifinal, and whoever wins that clash will progress to the finals of the tournament.
Vazir Khan made his debut for the State in the sub-junior category in 1979.
Zinedine Zidane's side produced a toothless attacking performance in drawing at home with Real Betis 0-0 on Saturday, its second scoreless stalemate in three rounds.
The NGO director Srikanth Veleti also donated the footballs to the players and encouraged them to pursue their dreams.
Ganguly had made his debut for the Blue Tigers in the 1969 Merdeka Cup against Burma in Kuala Lumpur, on November 2.
In a low-key Premier League encounter, the result was settled by a mistake from goalkeeper Leno when he allowed Richarlison's cross through his legs and diverted it into the net, DPA reported.
On a disappointing night at the Jawaharlal Nehru Stadium in Fatorda, a new-look FC Goa took to the pitch with head coach Juan Ferrando making eight changes to help his players recover from the fatigue
Ángel Correa and Yannick Carrasco scored a goal in each half to secure a 2-0 home victory for Atlético, which moved three points in front of second-place Real Madrid
Although the plans for a Super League appear to be dead in the water with all of the original 12 clubs involved, apart from Real Madrid and FC Barcelona, pulling out in the face of widespread opposition, Real Madrid president Florentino Perez
The Atalanta earned a series of chances later, but poor finishing let them down. Atalanta's task was made harder after Gosens collected his second yellow card after trampling on Jordan Veretout.
The European Super League's announcement on Sunday, made by 12 founding clubs including Manchester City, Chelsea, Arsenal, Liverpool, Manchester United, and Tottenham Hotspur, was met with widespread criticism.
They are level with Atletico Madrid on 70 points but have a better head-to-head record than Diego Simeone's side, who face Huesca on Thursday, DPA reported
"We are going to keep working,” Pérez told Spanish radio network SER in an interview after midnight local time