The Union are now out of the MLS play-offs following the defeat but Nowak was proud of his players after an unlucky two-legged series.
"During this game, we weren't the worse team," he said after the 1-0 defeat at Robertson Stadium.
"Houston didn't overcome us with something we didn't know. They didn't come with anything that showed they were a better team. I think in both games we played better."
Nowak did, however, rue his side's lack of efficiency in front of goal, suggesting that was the reason the Union's season is now over.
"I think we stretched them pretty good," Nowak added. "The movement was very good.
"We just missed a couple of chances to deliver the ball faster from the wings. I think on a couple of chances, we should have done better."