Ferris, who played every game of Ireland's RBS 6 Nations campaign, suffered the blow during Ulster's 45-7 win over Aironi and is not expected to recover in time.
Willie Faloon is likely to start at openside, with Chris Henry at blindside and Pedrie Wannenberg completing the back row.
"The scan revealed significant damage to Stevie's left ankle and it is unlikely that he'll be available for Sunday," said an Ulster spokesman.
"That the game is on a Sunday, and therefore provides an extra day of healing, provides some hope but it remains very unlikely."
The 26-year-old's injury is a real blow for Ulster as they look to book a place in the semi-finals at the expense of Munster, who have Ireland trio Paul O'Connell, Conor Murray and Donnacha Ryan back from injury.
But Ulster lock Johann Muller insists regardless of what team each side manages to field there will be few surprises.
"This will be the first time the clubs have met in the Heineken Cup but we play them regularly in the domestic league so we know what to expect from them and there should not be any great surprises for either team," he said.
"However, the quarter-final is going to be incredibly tough, no doubt about that, but if we want to go at least one better that than last year then we have to go to Thomond Park and get the win that would take us into the last four."