Federer's shock loss to world number 116 Stakhovsky on his Centre Court stomping ground brought the curtain down on his run of 36 consecutive Grand Slam quarter-final appearances, which started at Wimbledon 2004.
World number 116 Sergiy Stakhovsky of Ukraine stunned 7-time Wimbledon champion Roger Federer 6-7, 7-6, 7-5, 7-6.
Day 3 of the 2013 edition of Wimbledon saw Maria Sharapova eliminated while the likes of Victoria Azarenka had to pull out due to injury. (All AP and AFP Images)
Maria Sharapova also took medical time-outs during her Round 2 game against Michelle Larcher De Brito.
World number 131 Michelle Larcher De Brito beat Maria Sharapova 6-3, 6-4 to make it to the Round of 32.
Injured second seed Victoria Azarenka was forced to withdraw from Wimbledon on Wednesday just minutes before she was due on Centre Court to play Italy's Flavia Pennetta for a place in the third round.
The 12th seeded Ana Ivanovic, who made the Wimbledon semi-finals in 2007, was beaten 6-3, 6-3 in 63 minutes by the 19-year-old Bouchard, who is making her main draw debut at the All England Club.
Croatian 10th seed Marin Cilic joined the list of Wimbledon's walking wounded on Wednesday when he withdrew with a left knee injury.
French sixth seed Jo-Wilfried Tsonga was forced to retire from his Wimbledon second round match against Latvia's Ernests Gulbis with a knee injury.
World number 189 Dustin Brown stunned higher ranked and former Wimbledon Champion Lleyton Hewitt 6-4 6-4 6-7 6-2 in the second round to enter last 32 of a Grand Slam for the first time in his career.
Eighth seeded Indo-Austrian pair of Mahesh Bhupathi and Julian Knowle advanced to the second round beating unseeded Argentine-Spanish duo Leonardo Mayer and Albert Ramos 6-2, 6-7(5), 6-4, 6-2.
14th seeded Indo-French pair Rohan Bopanna and Edouard Roger-Vasselin beat experienced Finnish-Russian duo Jarkko Nieminen and Dmitry Tursunov 7-6(5), 6-2, 7-6(6) in the first round.
In the women's doubles, Indo-American sixth seeds Sania Mirza and Liezel Huber beat Czech pair Renata Voracova and Klara Zakopalova 6-3, 3-6, 6-1 to advance to the second round.