Championship top scorer, Chris Wood, pounced in the fifth minute of additional time to snatch all three points from the hosts.
The Spaniard admitted the late goal was difficult to take, emphasising that the goal was scored at the very end of the game.
Benitez said he"did not understand" many decisions that he had seen in recent weeks, including the five minutes of stoppage time this evening.
He went on to say,"When you analyse the last games, the rules must be changing."
When asked if he thought five minutes was 'unfair', Benitez responded by saying "Have you seen anything special?" relating to notable stoppages in play.
Proud of the players
Despite the last gasp goal conceded, Benitez was full of praise for his players.
The 56-year-old said he was pleased with the "performance, commitment and passion" of his side, who dominated proceedings from start to finish.
"We created enough chances to win the game, we have seen this many times this season," added Benitez.
The Magpies controlled the game throughout, having 19 corners to Leeds' zero. The home side were very unlucky not to take home all three points.
Opposition boss, Garry Monk, was the happier of the two coaches after the game, insisting he felt the added time decision was "fair."
However, the former Swansea City defender was keen to put more praise on his young players, who "dealt with the atmosphere on St. James' Park."
Monk went on to say he was sure Newcastle would end up being promoted, but also said he fancied the chances of his Leeds side in the play-offs.