The Saints held a two-goal lead at White Hart Lane on Sunday before Spurs turned the game around to claim the points.
"The first half we were dominating, 2-0 up, and the referee decisions that did not go our way and the decision before the second goal changed the dynamic of the game," the Argentine is quoted as saying by BBC Sport.
"It was more that we lost the game than Tottenham won the game and there was help from the referee.
"Tottenham are a team that are equipped to win the Premier League, we are a young team, there is a long-term project for us, but despite that, it was an even-sided game and we were disappointed with today's result."
Southampton return to Premier League action on Saturday at home to Newcastle United.