The beleaguered Spaniard pointed to Ba's premature departure on his return to Tyneside as the pivotal moment in a game which the Magpies won 3-2 courtesy of Moussa Sissoko's last-gasp strike.
Ba felt the full force of the Argentina international's boot in his face as the pair challenged for a 32nd-minute loose ball, which the striker headed inches wide with the score at 0-0.
Benitez, whose side has now not won in four games in all competitions, said: "It was a penalty and a red card for me, the incident.
"In the middle of the park, you just carry on and go back from a free-kick. In the penalty area, you go back, penalty and red card.
"It changed the game. We lost one player with a broken nose, we had one substitution and we had a great reaction in the second half, but it was not enough."
Defeat on Tyneside left Benitez under ever greater pressure. However, he was refusing to be bowed by the criticism despite seeing his team fail to hold on to a lead for the second time in four days.
He said: "We are doing a good job in terms of what you can see on the pitch. The team is doing well.
"The team has a very good team spirit and that is really positive and I am confident we will finish in the top three. I will do well.
"What I know, what I can see is the team doing well, working hard and when we have this advantage, we have to manage in a better way."