The Manchester United striker was ruled out after suffering an ankle injury during the English Premier League leaders' 2-0 loss at Fulham on Saturday and will also miss the home tie in Group Eight against Cyprus in Sofia on April 1.
"Unfortunately, we've lost our most important players," said Stoilov, who has also been deprived of winger Martin Petrov and defender Alexandar Tunchev.
"But this is the reality, we can't change it and we have to do everything possible to win against Ireland," Stoilov told a news conference.
Stoilov said Berbatov would be replaced by Hertha Berlin striker Valeri Domovchiyski and Aston Villa midfielder Stilian Petrov would wear the captain's armband.
"We know it's an extremely important match for us," said Stoilov. "Ireland are a well-organised team and I want to see us being brave in attack."
Bulgaria are third in Group Eight with three points from three draws, seven points behind leaders Italy and Ireland who have both played four.
Stoilov believes Bulgaria will not lose all hope of reaching the 2010 finals in South Africa even if they lose to Ireland.
"I did a lot of calculations and I know we can qualify even if we lose in Ireland but this is the worst scenario and I'm not considering such an outcome," he said.
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