The 32-year-old American second seed was outplayed by Moya who booked his place in the Masters Cup in Shanghai with an almost flawless performance.
Agassi, who is 43 points behind Australian Lleyton Hewitt in the Champions Race, lost the first set to a single break of service and fell behind in the second.
A pumped-up Agassi was given a warning for swearing at the umpire as he served at 2-2 in the second set having just broken back, and for a while he threatened to turn the match around in front of a frenzied centre court crowd.
The 10th-seeded Spaniard, who saved six match points to beat reigning champion Sebastien Grosjean on Thursday, kept his cool, however, and broke the American again at 3-3.
Agassi had three break points as Moya served for the match, but failed to make them count, the Spaniard clinching victory on his second match point after one hour 21 minutes on court.—Reuters