Pune FC have collected four points from two matches while Bagan have logged only two points from as many games. They now have an uphill task of winning both their remaining group league games in order to have any chance of making it to the last-four stage.
The green and maroon brigade, who had better share of scoring opportunities, took the lead through Pierre Boya in the 26th minute and Ryuji Sueoka restored parity for Pune FC from the spot in the 66th minute.
Pune FC coach Karim Bencherifa started with Sueoka and Eric Brown in attack while Matthew Gonsalves and Luciano Sabrosa filled in at the heart of defence.
His counterpart Sanjoy Sen had Boya partnering Chennayin FC's Balwant Singh in attack while Lalkamal Bhowmick was expected to sit deep as the defensive playmaker in the team.
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Bagan who drew their first match against Bengaluru FC were looking forf full points started on attacking note as Sony Norde delivered a perfect cross in the box which was headed by Balwant to Boya, who could only volley it straight to Amrinder Singh in goal, within five minutes of the start.
Bagan who probed into the rivals had another chance to surge ahead in the 20th minute but Balwant header went over.
Five minutes later, it was Sony Norde again who orchestrated the attack from the left and had his shot blocked by Laramluaha Hmar before Pierre Boya skied his effort from close range.