Tensions were high throughout the match with both players going back and forth as they went all out for the win.
In the third and final set Del Potro could be seen giving Federer a long stare after the Swiss star smashed a half-volley into his leg.
But it was in the second set when both players let their frustration out.
Del Potro had taken the first set and was on the verge of winning the match in straight sets as the second went to a tie-break.
Federer was left furious by a call he thought was out and smashed his racket on the floor even when hawkeye proved the decision was correct.
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Del Potro too aimed some frustration towards the umpire as he appeared to lose his temper regarding noise from the crowd.
Federer went on to force a third and final set and had two championship points before the Argentine fought back to win his first Masters title.
The tensions between both players clearly dissipated after the game and Del Potro joked about how angry he was during the second set.
“I can not believe I am here with this trophy and beating Roger after a great battle,” Del Potro said.
“I was really angry after the second set but I was lucky in the last tie break.
“I played well and finally I got the trophy.
“Thank you to my team for staying with me in the good moments, bad moments and I share this trophy with you.”