After a goal each for Ivan Toney and Phil Foden in the first half, the Bees striker tapped home a 98th minute winner to consign City to a second loss of the league season.
We had 75% possession and created a host of chances throughout the match.
"The better team won," said Guardiola in his post-match press conference.
"We had a lot of problems and we could not press as they didn’t allow us. In this process when they gave it to the striker we could not do it.
"When Toney flicked the ball on while playing through the middle he created problems."
City started slowly, with Toney's 16th minute opener coming after several impressive Ederson saves.
We grew into the match from that point, eventually grabbing an equaliser through a powerful Phil Foden effort on the stroke of half-time.
Guardiola was happier with how his team performed in the second period but was always aware of the threat posed by Brentford.
He said: "We saw in the first action and the first 15 minutes they had two clear chances.
"After that we played better and played a bit quicker. We started the second half well but every time they break with long balls we could not do it.
"It was quite similar last season when they were here. We struggled to create as their structure defensively is so deep they force you to go outside and they defend crosses really well."