Beckham picked up the injury playing for the LA Galaxy against Mexican team Pachuca on Wednesday.
After a scan on Thursday, the team said in a statement that he had suffered a sprained medial collateral ligament in his right knee and was ruled out for about six weeks.
England will play Euro 2008 qualifiers against Israel on Sept. 8 and Russia four days later.
England manager Steve McClaren is already without key striker Wayne Rooney of Manchester United, who has a hairline fracture in his left foot.
In the latest setback to his injury-hampered career in the United States, Beckham was substituted in the 33rd minute of the Superliga final after a challenge with Fernando Salazar.
The 32-year-old midfielder arrived at Galaxy in July struggling with an ankle injury he picked up playing for his country against Estonia in a Euro 2008 qualifying match in June.
Beckham aggravated the injury in his final appearance for Real Madrid 11
After a delayed start to his American adventure, Beckham missed Sunday's Major League Soccer match against Colorado Rapids after limping off Thursday's game against Chivas USA.
The former Manchester United player had lined up against Chivas the day after playing the full 90 minutes in England's friendly against Germany at Wembley stadium in London and then flying back to LA.
Beckham said his latest injury was a result of him not being fully fit.
"I was overcompensating (for the ankle) and went into the tackle a little bit weaker than I would have done fully fit," Beckham said in comments reported on Galaxy's Web site.
In his post-match comments, Galaxy coach Frank Yallop conceded that Beckham had been playing while not fully fit.
"David is playing with an injury. He shouldn't be playing, to be honest and I'm sticking up for him here," Yallop said.
"He's hurt but he's playing and that shows the character of him and it shows the character of the team because he lifts the play of the team when he plays."