After the two sides were tied 2-2 at half time, it was in the 55th minute when Alan Rodriguez successfully converted from the spot to score the winner for Paraguay.
Rodriguez fired past Mali goalkeeper with a powerful spot-kick after Paraguay were awarded a penalty courtesy Abdoulaye Diaby's handball.
Mali had their chances, but on most occasions, their players shot above the bar from long distances.
Earlier, Paraguay took the lead in the 12th minute courtesy a stunning strike by Antonio Galeano.
A free kick by Julio Baez, was punched by the Mali custodian outside the box, which was calmly controlled by Galeano, who took the ball on his chest and shot a thunderous volley past the goalkeeper with his right foot.
Paraguay were rewarded for their aggressive style of play from the start.
Five minutes later, a defensive mistake by Mali helped Paraguay scored their second goal and take a 2-0 lead through Leonardo Sanchez's strike.
Three minutes later, Mali reduced the margin when Hadji Drame netted the ball. Salam Giddou, dribbled past two defenders and passed to Drame, who after a little dribble, slotted the ball with perfection in the 20th minute.
It was an intense first half with both the sides displaying attacking style of football.
Initially, Paraguay were more aggressive of the two, but after conceding two goals, Mali came back strongly.
In the 30th minute, Mali's Lassana Ndiaye ran in from a distance but his shot hit the crossbar and bounced away.
But it took another four minutes for the last edition's runners-up to equalise.
In the 34th minute, Djemoussa Traore showed blistering pace from the left flank, releasing Ndiaye, who netted the ball past a changing Paraguay goalkeeper.
Paraguay kept the Mali goalkeeper busy throughout the first half which ended in a 2-2 stalemate.
After the break, Mali had a definite chance, but Ndaiye ailed to get past the Paraguay goalkeeper, who came up with a good save.