FC Goa were in danger of exiting the league early this season but coach Zico masterminded his first win over a team coached by Antonio Habas as Brazilian striker Rafael Coelho scored the all-important goal from a free-kick in the 32nd minute at Balewadi Sports Complex Stadium here.
The win helped FC Goa move to the seventh spot with seven points from eight matches while FC Pune City are now at the bottom with six points from seven matches.
Habas, who had never lost a match against Goa, made three changes, at least one necessitated with the two-match suspension of defender D Ravanan.
FC Goa looked solid at the start, working their way neatly ahead. Joffre Gonzalez was presented with the first chance in the 10th minute when Pune lost the ball but the Spanish midfielder shot wide from close range after getting into a good position.
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Joffre won a free-kick just outside the box after being brought down by Pune defender Augustine Fernandes. Rafael stepped up and curled the ball into the far corner of the nets, past Pune goalkeeper Edel Bete who was distracted by the presence of Goa striker Robin Singh in the wall.
Pune came very close to securing the equaliser just before the half-time break as Jonatan Lucca cut past five Goa players but his shot was saved by goalkeeper Kattimani.
Goa had two good chances to kill the match but Joffre shot wide after being put clear by Rafael and the Brazilian striker was himself guilty of missing an easy chance after he cut past the goalkeeper but only ended up providing an opportunity for Pune defender Rahul Bheke to head the ball away from the goal-line.