Henry was also among three players shortlisted for the MLS Most Valuable Player award, to be announced on Thursday.
The others, Kansas City midfielder Graham Zusi and San Jose forward Chris Wondolowski, also made the Best XI, announced by MLS Commissioner Don Garber yesterday.
Beckham, who will leave the MLS after Saturday's Cup final against Houston, did not make the team.
American international Landon Donovan made the team for the fifth time in a row and sixth overall.
MLS Best XI 2012
Goalkeeper: Jimmy Nielsen (Sporting Kansas City)
Defenders: Victor Bernadez (San Jose Earthquakes), Matt Besler (Sporting Kansas City), Aurelien Collin (Sporting Kansas City)
Midfielders: Osvaldo Alonso (Seattle Sounders), Landon Donovan (LA Galaxy), Chris Pontius (DC United), Graham Zusi (Sporting Kansas City)
Forwards: Thierry Henry (New York Red Bulls), Robbie Keane (LA Galaxy), Chris Wondolowski (San Jose Earthquakes).