The Australian international managed to get through 90 minutes of the 2-1 extra-time loss, which gave Houston Dynamo a 4-3 aggregate victory in the Eastern Conference semi-final.
Cahill, who scored in the first leg on the weekend, sustained a thigh and hamstring problem during the match but is hoping he can be fit enough for the Socceroos' friendly with Costa Rica next week.
"I cramped up in my thigh towards the end. I had someone step on me in the last game and tonight in the second half of extra time I just seized up when I jumped," Cahill told AAP.
"I felt a cramp just on my thigh underneath my hamstring. I couldn't straighten my leg so I was struggling to run. I couldn't believe it.
"I couldn't do anything. I have no football now for six weeks other than playing for the national team and hopefully I will be ok for that. I'll patch myself up and go again.
"But to be honest I wasn't banking on having such little football to play."
The Red Bulls took out the 2013 Supporters' Shield after finishing the regular season on top of the MLS standings but are now out of the running for the MLS Cup after being beaten by the Dynamo, who have lost the past two cup finals to the LA Galaxy.
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