However, the Black Cats have confirmed that O'Shea will join up with the rest of Giovanni Trapattoni's Premier League-based players to start preparations in Malahide on Sunday.
O'Neill initially indicated that the defender had aggravated a long-standing calf problem, but a club statement revealed it was an ankle injury and there is no lasting damage.
A spokesman said: "John suffered a knock to his ankle in training prior to the Fulham game, which he aggravated slightly in Sunday's game against Manchester United.
"He was taken off as a precaution and following positive results from a scan last night, he will meet up with the Republic of Ireland squad as scheduled next week."
O'Shea has been a cornerstone of Trapattoni's team in the last two qualifying campaigns, playing at both right-back and in central defence, and his absence would have been a major blow.
The Republic's Championship players, as well as Black Cats winger James McClean, will arrive at their training base on Thursday, and the remaining members of the squad will join up three days later.
They have a week in Ireland before a friendly against Bosnia-Herzegovina at the Aviva Stadium next Saturday, and will then head for their training camp in Montecatini, Italy, before a final warm-up game against Hungary in Budapest.
They open their campaign against Croatia in Poznan on June 10.