The final game, with Kasparov playing black, fizzled out into a draw after 27 moves.
Azerbaijan-born Kasparov, 40, tied his first game against "X3D Fritz," lost the second and then came back to win the third.
The Russian chess champion played wearing 3-D glasses, gazing at a chess board that appears to float in the air. He dictated piece movements with voice commands and rotated the board with a joystick.
Kasparov is considered the world's best chess player, even though he lost the world champion title to Vladimir Kramnik in 2000.
This is his third series against a computer.
He lost to Deep Blue in 1997 and tied with Deep Junior in February.
"X3D Fritz" is an upgraded version of "Fritz," the machine which took on Kramnik in Bahrain in 2002, tying him four to four.