The 25-year-old scored West Ham's only goal in the 1-1 result, with the second leg to be played in France next week.
"We weren't at our best this evening, but it's all still to play for," Bowen told BT Sport.
"The manager said at half-time to keep our heads because we weren't happy with the decision obviously. It was a case of staying in the game.
"We did, went 1-0 up and it was then just about defending the lead. It was always going to be difficult. It is still all to play for."
He added: "I said before the Sevilla game when I was here watching, it was an unbelievable night.
"But as a player, you want to be on the pitch, you want to be having these moments. The boys did superbly to get through the round before.
"Tonight, again, the atmosphere was unbelievable. It was killed a little bit with the red card, which we knew was always going to be difficult. I'm sure we'll take a lot of away support on next week and try and get into the semi-finals."