A tense and cagey goalless first half led to a more frantic second and Spurs, on top for the majority, made the breakthrough and added to it within two minutes with the Gunners showing little response.
The 2-0 win confirmed Tottenham would finish above Arsenal for the first time in Arsene Wenger's reign, a run dating back 22 years.
"There’s nothing I can say today," Henry said on Sky Sports. "You have to go home and accept Tottenham were the better team today. It’s a missed opportunity in a special game against Tottenham."
Henry is concerned by Arsenal gameplan under Wenger, with the manager reverting to a three-man defence in recent weeks.
But the former striker and club coach questioned the long-ball approach adopted at White Hart Lane, insisting it is against Wenger's previous long-standing tactics.
He continued: "The thing that worries me the most is the way they are playing. The back three looked like it was all over the place.
"Arsene used to say he wanted to play against teams that played against him, not teams that play all at the back, anti-football. What I saw here was, especially in the first half, Petr Cech bypassing the midfield and going long to Olivier Giroud all the time.
"Something I saw that was well prepared was on Tottenham goal kicks they were going really high to force them to go long.
"You cannot play in a back three and just expect it to work well in three or four games. It takes time. From what I’ve seen I wasn’t reassured because of the way they played."