The sides will renew acquaintances at Salt Lake Stadium this weekend this weekend, having faced off in the regular season on Wednesday - playing out a 1-1 draw.
Fikru Tefera's late penalty ensured the hosts gained a point while ensuring the visitors could only finish second as opposed to first.
Leaders Chennaiyin held onto first place and will meet Kerala Blasters on Saturday in the other semi-final first leg.
Ahead of the second meeting between Goa and Atletico in seven days, Zico played down the idea of his side being at a disadvantage from finishing second.
The former Japan coach made a number of changes for the clash, having already sealed a top-four finish, and was full of praise for his team.
"I am not disappointed. We have qualified for the semi-finals; that is more important," he said after the draw in Kolkata.
"I hope to get to first place at the end and win the final.
"There is no advantage or disadvantage [to finishing first or second]. I am very happy. They played beautifully.
"I have been saying since the beginning: we have 27 good players, not just 11."
Having taken 13 points from their last five games, Goa undoubtedly go into the semi-finals as the form team, with Chennaiyin needing to regroup ahead of their clash with Kerala on Saturday.
While Kerala left it late to seal a top-four spot with a win over Pune City, the leaders have won just two of their last five outings.
Marco Materazzi's men surrendered a two-goal lead to draw with Delhi Dynamos on Tuesday, but will hope to make it three wins out of three against Kerala on Saturday.
Materazzi has a fully-fit squad to choose from and stated he was not surprised to see Kerala extend their season.
"They are a very good side and have a good record at home," he told a news conference.
"I said before our league match in Kochi that they will be in the semis so I am not surprised."
