Paris St Germain star Ibrahimovic grabbed his fourth goal in the 4-2 win with a wonder goal in the closing seconds but Hodgson felt that merely underlined a night when little went in favour of the visitors.
Goals from Danny Welbeck and Steven Caulker had overturned an early deficit as England led before sweeping changes allowed the hosts to wrestle control again.
While admiring the technique of Ibrahimovic's opportunist strike, it will never sit well with the Three Lions boss.
"I was not very happy about it, I was still smarting a bit from the free-kick, I thought it was a bit harsh on us. I thought 2-2 was harsh, let alone 2-3," Hodgson said.
"It was a fantastic effort on his part, and I admire the athleticism and the technique, but he did not have a lot to lose.
"It was the last kick of the game. If the ball had gone 75 metres into the stands, who cares? If he had missed it completely, who cares? The ref was going to blow his whistle as soon as it happened."
Hodgson continued: "For me it was the final humiliation in a way in a game where I did not really believe the Swedes deserved it.
"Okay, good luck to them it was their night and the opening of their stadium, but if I had been the Sweden coach, I would have been thinking how on earth did we pull this one off?"
Hodgson has certainly been through his share of headlines since being installed as Fabio Capello's successor in May, one of which surrounded a conversation with a fan over the international future of Rio Ferdinand while travelling on the tube.
"I suppose you have to be very careful what you say. On that occasion, it was an error of judgement," Hodgson said during a Q&A session in a function held at Norwich City Football Club.
"It was just to answer a question relatively honestly, the man should have been told either it was none of his business or to wait and see, but I cannot take it that harshly.
"I was a bit disappointed, of course, but I would be even more disappointed if it means I have now got to be a prisoner in my own home, and that I can only travel by luxury limousine and forget that trains exist, because where my wife and I live, travelling by train up to London is certainly the easiest and fastest way of travel, so I will just have to be a little bit more careful in future.
"All of the people I have spoken to have been pleasant, their questions have been fair and honest.
"It was a bit unusual I suppose that there just happened to be an undercover journalist who just happens to find himself on the same train and just happens to find himself a little scoop.
"He had a great night, I had a slightly lesser one, but I hope I won't meet too many of those undercover journalists in the future."
Hodgson must now cross his fingers that key players avoid serious injury and get through unscathed to the February 6 friendly with Brazil, and more importantly, the key World Cup qualifier double-header against San Marino and Montenegro in March.
The England manager said: "I work with some very talented players and am very optimistic about the future."