The actions by Beckham, who was also fined an undisclosed amount, occurred during and immediately after his team's 4-3 loss and were considered unacceptable and detrimental to the league's public image, the MLS said in a statement.
With under a minute remaining in stoppage time, an impatient Beckham kicked a ball San Jose's Sam Cronin, who was lying on the pitch. The ball hit Cronin and referee Hilario Grajeda, resulting in a yellow card for Beckham.
Cronin, who had been writhing on the ground while clutching his face, immediately sprang to his feet to remonstrate with the former England captain.
The infraction earned Beckham, who had to be separated from opposing players after the final whistle, an automatic one-game ban for yellow card accumulation, which he served earlier this week.
The 37-year-old, who has been omitted from Britain's squad for the London Olympics, will serve his one-game ban on Sunday when the Galaxy visit the Chicago Fire.
Thursday's ban was the latest blow in what has been one of the more trying weeks of Beckham's career.
The former Manchester United, Real Madrid AC Milan and England midfielder had been expected to be included as one of the three over-age players in Stuart Pearce's team for the London Games.
Chief London Olympic organiser Sebastian Coe is to discuss a "Games time role" with the globally recognised sports figure, who played an ambassadorial role in London winning the Olympics.