Long was ruled out for up to six weeks after sustaining a knee injury while playing for West Bromwich Albion against Aston Villa last weekend.
Ireland manager Giovanni Trapattoni has few attacking options as Kevin Doyle will miss the away leg in Tallinn on November 11 through suspension.
Robbie Keane was included in the squad after L.A. Galaxy said he may be fit to play in a game next week.
Ireland, which is vying to secure a place in the finals for the first time since 1988, are favoured to overcome Estonia, who sit 34 places behind them in the FIFA world rankings.
However, 59th-ranked Estonia, despite having never qualified for the finals of a major competition, impressed many observers with victories over Slovenia and Serbia in the group stages.
"There is no room for complacency," Trapattoni said. "These games will be a huge challenge for us and we must maintain the correct mentality from start to finish."
Ireland will host Estonia in the second leg in Dublin on November 15.
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