Celtic captain Brown was sent off just before the hour mark for a needless kick at Neymar after bringing down the Brazilian.
Lennon was unhappy with the decision, feeling there was not much contact made in the incident.
"It's not a red card," Lennon told Sky Sports. "I'm not convinced there was any contact there and it has changed the game.
"Again I am not convinced he did (make contact with Neymar). (I am) maybe not so happy he may have put himself in that position in the first place but looking at it again it's nothing.
"There was a lot more going on in the game that warranted a lot more than what Scott got tonight."
Asked if it was impossible to get a result after being reduced to 10 men, Lennon added: "It's not impossible because we created two brilliant chances. It is really difficult playing against Barcelona with 11 men, it's even harder with 10.
"The game got stretched in the end. We went for it - I would rather lose 2-0 going for it than see the game out 1-0 and you saw the quality of my goalkeeper in the end as well.
"We were always in the game right up until the last kick of the ball.
"We restricted Barcelona, we knew they would have possession for periods of the game but up until they scored we had the better chances.
"I thought we were terrific. Our defensive shape was good, our discipline was good and we had a real spell there with James (Forrest) and Charlie (Mulgrew) with two great chances, although Valdes has made a wonderful save but Charlie maybe should have done better with the header.
"Sami (Georgios Samaras) had a great chance in the first 10 minutes and Valdes again has come out and smothered it."
The defeat leaves Celtic with two defeats from their opening two games in Group H, but Lennon was boosted by AC Milan's draw with Ajax in Amsterdam and the Celtic boss admits their double-header with the Dutch side is crucial to their chances of progressing to the knockout stages.
"It's a good result for us - it keeps the other two teams closer to us.
"If Milan had won it might have been really difficult to catch them so the double header with Ajax is vital. We need to try and get four points from that if we can and then we've got Milan at home which is going to be a difficult game for them."