The loss of the third seed as he trailed Swiss qualifier Michael Lammer 3-1 in the first set followed the withdrawal from the Auckland event on Monday of Argentina's David Nalbandian with an abdominal injury.
The Spaniard is unsure if he will be able to recover in time for the Australian Open next week, but is hoping for the best.
"They say it's not too bad, I will have to wait three or four days with some ice, take some anti-inflammatories and see how it goes," Ferrero told reporters.
"I want to play over there so I will do everything in my power to make it, but we'll see. I cannot tell you now."
World 209 Lammer now faces a quarter-final against eighth seed Albert Montanes, who beat local hope Rubin Statham 7-6, 6-2.
Seventh seed Juan Monaco and Spanish compatriot and fourth seed Nicolas Almagro also fell as the line-up for the quarter finals was decided.
Tall American John Isner served 11 aces and five breaks of serve to beat Monaco 5-7, 6-4, 6-3.
France's Marc Gicquel, ranked 58 in the world, ensured a miserable day for 26th ranked Almagro with a 6-0, 6-3 thrashing.
Spanish top seed Tommy Robredo, coming off a Hopman Cup victory in Perth, was not at his best but good enought a quarter-final spot with a hard fought 7-6, 7-6 win over German Simon Greul.
Fifth-seeded German Philipp Kohlschreiber stayed on course to repeat his 2008 Heineken Open victory, with a 6-4, 6-1 win over Brazilian Thomaz Bellucci.
Kohlschreiber converted five of his six break point opportunities to ensure his fifth quarter-final in six appearances in the ATP event.