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 the Blues 13 points adrift of Barclays Premier League leaders Manchester United, having played a game more, and 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 that 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."
Newcastle went in at the break leading by the only goal, Jonas Gutierrez's 41st-minute glancing header, and only the most churlish of Chelsea fans could have begrudged them their advantage.
However, the European champions returned in determined fashion and turned the game on its head inside six minutes early in the second half.
Frank Lampard blasted them level after 55 minutes, his 10th league goal of the season for the 10th successive campaign, and when Juan Mata curled home a delicious second, the writing looked to be on the wall for the Magpies.
However, Alan Pardew's men, who launched what they hope will be a concerted fight to stave off relegation with a 2-1 win at Aston Villa in midweek, refused to accept their fate as January signing Moussa Sissoko, making his home debut, took it upon himself to inspire a dramatic finale.
It was he who reacted first after Petr Cech could only parry Yoan Gouffran's shot to steer home the equaliser and then, after he had twice tested the keeper following powerful solo runs, established himself firmly in the affections of the Toon Army.
There were only seconds of normal time remaining when the France international exchanged passes with full-back Davide Santon and then dispatched a low drive past the helpless Cech and into the back of the net to snatch victory.
Asked if he had seen a better home debut, Pardew replied: "Not since I have been here.
"[Papiss] Cisse made an instant impact when he arrived, but our fans, who are an intelligent set of fans - these people love their football here.
"They told me last time [in the 2-1 home defeat by Reading] that they didn't like me, that my subs were all wrong - and they were probably right.
"But they know a good player when they see one. He didn't just give us the goals, he gave us a lot more than that.
"I remember seeing him at Toulouse about 14-16 months ago and there are only two players that I have seen that I was desperate to get here. One was [Yohan] Cabaye and one was Sissoko, and we have managed to do that."