The 27-year-old world number 116 went down 6-2, 2-6, 7-5, 6-3 to experienced Austrian Jurgen Melzer in the third round.
Instead of the Centre Court, where he had ended Federer's run of 36 successive quarter-final appearances at the majors, Stakhovksy was exiled to Court Three where his challenge wasn't helped by falling heavily on the slippery surface.
That required his ankle to be strapped and his challenge eventually petered out as 32-year-old Melzer reached the fourth round for the second time in his career where he will meet dangerous Pole, Jerzy Janowicz.
The 24th-seeded Janowicz made the fourth round for the second successive year by beating Spanish 15th seed Nicolas Almagro, 7-6 (8/6), 6-3, 6-4.
Britain’s Laura Robson made the third round with a 6-4, 6-1 win over Colombian qualifier Mariana Duque-Marino and goes on to face Marina Erakovic of New Zealand for a last-16 spot.
Ferrer, Haas through
Spanish fourth seed David Ferrer, meanwhile, reached the third round with a 6-3, 3-6, 7-6 (7/4), 7-5 win over compatriot Roberto Bautista Agut in match held over from Thursday because of rain. Heavy rain also delayed play on the outside courts yesterday with Bulgarian 29th seed Grigor Dimitrov staging a temporary sit-down protest to register his anger at conditions on Court Three before he lost a five-set second round thriller.
German veteran Tommy Haas ended Jimmy Wang’s hopes of a first Grand Slam third round appearance as the Taiwanese qualifier was crushed 6-3, 6-2, 7-5.