In the 76th minute, with the home side leading through a Teemu Pukki strike - his first since notching against St Johnstone in September - the Honduras international went tumbling in the opposition box after going past Easter Road stopper Michael Nelson.
After Madden reached for the yellow card instead of pointing to the spot, the Celtic boss threw his jacket off as he moved down the touchline in rage and was given a talking to by the official.
However, afterwards Lennon was contrite when asked about the referee.
"I thought the referee had a good game," he said. "I got it wrong, he quite rightly booked Emilio.
"It was an excellent refereeing decision and I thought he had a good game.
"Even Garry (Parker, Celtic coach) thought at the time (it wasn't a penalty).
"I thought it was a penalty but looking at it again it is clearly not so the referee got it spot on.
"It is a natural reaction (from Emilio), there was a leg dangled out and he went over it so I don't think I need to speak to him."
Lennon hopes Pukki's goal will help the 23-year-old Finnish striker, signed from Schalke in the summer, overcome his natural shyness.
He said: "Hopefully it will give him a boost. It was a good striker's goal, I was really pleased with that.
"He is a shy boy by nature, we just want to eke more of his personality out, on and off the field and scoring goals is a great way of doing that, although I have been pleased with his contribution at times.
"You speak to him and tell him to be himself and interact with the rest of the players but it is difficult to change people's personalities.
"The boys are a good bunch and try to integrate all the players and you can see more and more of his personality coming out.
"I think he has something to offer and the only way we can get that is by playing him and him gaining confidence from playing with the rest of the players, same with Nir Biton."
Asked if Pukki has perhaps suffered in comparison to Gary Hooper, who was sold to Norwich in the summer, Lennon replied: "Yes. They are two different types of players.
"Who knows, he might kick on and get a run of goals and games, that is what we are hoping for.
"Gary was a great find for us and went on to be a top player so we are hoping Teemu can eventually become the same."
Pukki admits confidence has been a problem.
He said: "It is the job of a striker to score goals so of course you think of that (confidence) but now I have scored I can start playing like normal."
Hibs manager Terry Butcher's unusual pre-match team talk ultimately failed to pay dividends but he is happy with the progress of his side since he took over at Easter Road last month.
He said: "It's about building strong foundations, like you do with a house. Once you do that you add all the glamour bits.
"That's the pace, the craft with wide players and strikers.
"But we're not going to build a two-up, two-down. We're going to build a luxurious penthouse building.
"I sound like I'm off on one again but in my team talk today I was the same.
"I'm not sure any other manager has mentioned Lawrence of Arabia, George Washington and David and Goliath.
"I mentioned all three. I had to wake the boys up to get them on the bus, right enough, but it was funny.
"I'm just enjoying it, it's great. I'm getting everything from the players.
"Celtic were putting the ball into the corner at the end, hanging on for a 1-0 win and that says a lot for how far we've come."