The 30-year-old suffered a groin problem and limped out of the final training session in Malahide before the squad flew out to Skopje.
However, Trapattoni has named skipper Keane in his starting line-up and admitted that, while he still has a niggling doubt over his captain, it is a small one.
The Italian said on Friday: "We have only, I hope, a little doubt about what happened yesterday.
"I think we can have a check today, but we have also one day to decide if it will be possible for Robbie to play.
"I hope he can because it is important for us that he can play."
Keane's appearance alongside his manager at Friday afternoon's press conference at the Philip II Stadium was a clear indication of his own feelings on the matter.
The striker, who took his international goals tally to 49 with his Carling Nations Cup winner against Scotland last week, said: "It feels a lot, lot better than it was yesterday, but in terms of being fit, I would say definitely, yes."
Keane will partner Simon Cox in attack as the West Brom man makes his competitive debut ahead of Reading's Shane Long, while Keith Andrews has got the nod to link up with Glenn Whelan in central midfield.
Stephen Kelly will start at right-back with veteran Kevin Kilbane on the left and Darren O'Dea lining up alongside John O'Shea in the middle.
Republic team: Given; Kelly, O'Shea, O'Dea, Kilbane; Hunt, Andrews, Whelan, McGeady; Keane (captain), Cox.