Italian media speculated that the Argentine - 40 in August - could be out for up to eight months and that, considering his age, the injury could even spell the end of his career.
"There's an injury to the Achilles tendon of his left foot. It's a big blow and we really didn't need this injury to Javier," Stramaccioni told Inter's website (www.inter.it) following the 1-0 defeat.
"Losing him today certainly hurts us in a very difficult moment."
Reports said Zanetti, who is two years older than his coach, would have to wait until the team return to Milan to discover his fate following an MRI exam.
The remarkably consistent Zanetti has made more than 800 appearances for Inter, including over 600 in Serie A, since joining the club from Banfield in 1995 and has never before suffered a serious injury.
He has won five Serie A titles, four Italian Cups, one Champions League, one UEFA Cup and one Club World Cup and is also Argentina's most capped player.
"I felt a pull at one point, I'm not sure if anyone touched me, and it really hurt," Zanetti told Mediaset Premium. "I will overcome this as well."
Inter have suffered a string of injuries in the last few weeks and were missing Rodrigo Palacio, Diego Milito, Walter Samuel, Antonio Cassano, Walter Gargano and Fredy Guarin for the trip to Sicily.
In the last few weeks, Stramaccioni's team have dropped to seventh in Serie A, ending their hopes of Champions League football next season, been knocked out of the Europa League by Tottenham Hotspur and been beaten by AS Roma in the Italian Cup semi-final.
"It's a curse," agreed defender Andrea Ranocchia, who took the armband from Zanetti in the 17th minute. "We seem to be losing two players a game. It's just incredible.
"With the misfortune that we have been suffering, we just have to give more. We have four games to go and we're in an emergency."
- Sports & Recreation