The 30-year-old Makarova took down Wozniacki 6-4, 1-6, 7-5 to bring the Danish star's tournament to a surprisingly quick conclusion.
"I think I did everything I could", Wozniacki said.
Wozniacki's defeat by Ekaterina Makarova together with Sloane Stephen's first-round defeat on Monday means Simona Halep will remain as world number one even if she too joins the long list of title contenders to bite the dust.
Roger Federer extended his flawless winning streak at Wimbledon to 26 consecutive sets as the defending champion crushed Lukas Lacko, while Serena Williams powered to her 16th successive win in Wednesday's second round action.
Roger Federer's Wimbledon dominance is showing no signs of weakening as he breezed into the third round.
After the 36-year-old American won the 2017 Australian Open, five different players won the next five women's majors. "Sometimes your serve matches up better against certain players".
In total, the eight-time champion lost only nine of 61 points on his serve and broke Lacko five times, including with a forehand victor to close out the match.
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Federer won 35 straight points on his own serve en route to beating Lacko and advancing to the third round.
"I played very well again, I felt good out there, less nerves than in the first round, which is normal", Federer said, after racking up his 93rd Wimbledon win. While Donna Vekic beat Rebecca Peterson 7-5 6-4 and Yanina Wickmayer saw off Andrea Petkovic 6-4 6-3. "It's like 7-6 in the fifth and it's been like an hour and a half!"
Serena Williams of the United States returns to Viktoriya Tomova of Bulgaria during their third round match at Wimbledon on Wednesday.
Earlier, Karolina Pliskova outplayed Victoria Azarenka, a two-time Grand Slam champion, to reach the third round.
While the Centre Court crowd clearly appreciated the sight of Williams in full flow they took a shine to the plucky Tomova who battled hard to make a match of it.
"It was better than my first round and I'm happy that I'm going in the right direction", said 25th-seeded Williams.
Even ultimate warrior Williams, who was unable to defend her 2016 Wimbledon title past year because she was pregnant, applauded a couple of her opponent's winners late in the second set before completing victory in 66 minutes.