Garcia shot a 1-over 73 on the West Course at Wentworth on Thursday and then advised officials he was unable to continue.
The seventh-ranked Spaniard first felt pain in his knee during the final round of last week's Spanish Open. An MRI showed no serious damage.
Garcia says "on the 17th and 18th holes today, it didn't feel good at all. The problem is now is with the U.S. Open coming up. I don't want it to get worse."
The U.S. Open at Pinehurst starts June 12.