West Brom expect the Tipperary native to be out for six weeks, but Trapattoni hopes that the 24-year-old can recover from his knee problem in a third of that time.
Roy Hodgson understands why the Italian named Long in his squad yesterday, although he does not believe that the striker will be ready.
However, Trapattoni has opted to give the player every chance instead of summoning Best or additional striking cover, with the 72-year-old already coping with Kevin Doyle's first-leg suspension and doubts surrounding Robbie Keane's well-being.
"He said to me, 'I think it's not bad', but the manager and doctor say six weeks," said Trapattoni. His West Brom counterpart repeated that prognosis.
"There is nothing to stop Giovanni being optimistic," Hodgson said. "There have been lots of cases in the past where people have been diagnosed with an injury which will take longer than it actually takes.
"So no one would be happier than ourselves if Shane recovers in two weeks and can play for Ireland in these important qualifiers.
"I just hope they won't be too disappointed if the doctor's prognosis turns out to be the correct one."
If Long misses out, Stoke's Jonathan Walters has a strong chance of starting in Tallinn in two weeks' time. Trapattoni believes that Keane will be available and, while the 72-year-old is a big fan of Simon Cox and did partner him with his captain in June, he thinks they are similar players. So, the pace and physicality of Walters could be required to stretch an imposing Estonian rearguard.
Kevin Kilbane won't be involved in the play-offs and may have played his last game for Ireland after he was left out of the 26-man squad. Darron Gibson is recalled despite his inactivity at Manchester United.