The Nerazzurri paid the penalty as misfortune once again fell on the club's campaign when the Argentine had the opportunity from 12 yards but slipped at the crucial moment
The home side suffered a 3-1 defeat to the Biancocelesti - their first league defeat at San Siro against the capital club since 1998.
Sergio Floccari, Hernanes and Ogenyi Onazi were all on target for Vladimir Petkovic's side as Stramaccioni was left to rue what might have been.
"We lost another player to injury and the penalty of Alvarez sums up our season, we would have levelled the game if that went in,” he told Sky Sport Italia.
“Commenting on an encounter like this is not easy, we lost 3-1 in a match that we deserved at least a draw.
"We hit the woodwork and then Ogenyi Onazi scored a stunning goal.
"Even in our current condition, we tried to play the game and take the initiative right to the end. I saw an improvement in terms of performance.”
When asked directly about the mistakes made by Alvarez and Samir Handanovic, Stramaccioni refused to blame individuals for his side’s disappointing season.
“Alvarez had a good game, it happens even to the great players slipping on the spot," he continued.
"The error from Handanovic is not something I will even talk about it, he is a great goalkeeper and it can happen."
He also backed fans' right to protest against his side, after a result which confirms Inter’s absence from Europe next season.
Stramaccioni added: “The banners of the fans? Their civil protest is legitimate, they have the right to express their dissent.”