This was Henman's first clash with the Russian, although he knew beforehand that he was in for a tough match.
He added: "I had practised with him a few times before and I have seen the way he's been playing recently.
"He is in top form at the moment, he's won a few matches in a row. He played very well today."
Henman, who is ranked seventh in the world and who will take part in the Masters in Houston from 15 to 21 December, has enjoyed a relatively good season, reaching the semi-finals at both the French Open and the US Open.
He added: "My performance at Roland Garros was certainly the most outstanding moment of my season. I had never reached further than the third round there. It was a real breakthrough and I had a lot of fun.
"The clay surface is so different from my environment from home."
Henman is now aiming to finish the year on a high in Houston and is relishing the few extra days of rest his loss to Youzhny has afforded him.
"I never find anything positive about losing a match but at least I will have a few days off to rest and clear my thoughts before the Masters."
Youzhny, who recently won his second career title at St Petersburg, faces a quarter-final match against Radek Stepanek of the Czech Republic. He qualified with a comfortable 6-2, 6-3 win over No17 seed Vince Spadea of the United States.
In other matches, No2 seed Lleyton Hewitt was gifted a place in the next round when his opponent, Nicolas Massu of Chile, withdrew injured with the Australian 4-3 up in the opening set.
Guillermo Canas of Argentina, the 13th seed, advanced with a 7-6, 6-2 win over German Tommy Haas.
