Giovanni Trapatonni drafts the fit-again O'Shea, who has shaken off a hamstring problem, staright back into the team as a replace for groin-injury victim Stephen Kelly.
Kelly's club team-mate Damien Duff returned from Tallinn with a rib injury, but he was fit enough to train with the rest of the squad on Monday, while Doyle is available after suspension.
"I have said to the team to be careful. It will not be an easy game," said Trapatonni.
"It is another 90 minutes for our opponents. They lost some pride and it is important that we play with the same seriousness for our opponents and for the people coming to the stadium to watch the game.
"We have a duty to repeat this game, maybe not with the same goals, but for the Irish people.
"It is important that we play this game with the same seriousness for our opponents and for the people coming to the stadium to watch the game.
"At home, we can also play with more confidence now with this advantage, but with the same mentality."
The size of the mountain which Estonia - trailing 4-0 from Friday's first leg - need to scale has increased with the suspensions of defensive pair Andrei Stepanov and Raio Piiroja.
They must also cope without goalkeeper Sergei Pareiko who picked up a yellow in Tallinn last week.
Republic of Ireland team: Given; O'Shea, St Ledger, Dunne, Ward; Duff, Andrews, Whelan, Hunt; Doyle, Keane.