The 23-time grand slam victor claimed 84% of her first serve points, a good sign for the 36-year-old after the pectoral injury that ruled the American out of a blockbuster fourth-round clash with Sharapova at Roland Garros.
She served for the match, then had four match points at 5-4 before eventually getting the job done at the sixth attempt.
Canada's 13th seed Milos Raonic swept past Australian John Millman in straight sets, but in predictably attritional fashion, requiring three tie-breaks for victory.
When she came on to continue, the second seed took a 3-0 lead due to Makarova's unforced errors.
Ekaterina Makarova is next up for the Dane in the second round. She will face Lucie Šafářová in the round of 32.
Wozniacki memorably rallied from a 5-1 final set deficit, and saved two match points against little known Jana Fett in the second round in Melbourne, before going all the way.
"Wozniacki added, according to The Guardian: "(The match was) frustrating because I feel like I could have gone and done something really great here.
"There's so many things that I want to improve on, but that's kind of how I always feel", Williams said in her post-match press conference.
Croatian Donna Vekic followed up her win over another American Sloane Stephens with a 7-5 6-4 win over Rebecca Peterson.
"I was really nervous because Caroline will never miss and you need to win the points, play the winners", Makarova said.
The Swiss champion was at his breath-taking best as he crafted 48 exquisite winners during a 90-minute match that seemed more an exhibition of his shot-making than a charge towards a record ninth Wimbledon title.
Karolina Pliskova won the battle between former world No 1s against Victoria Azarenka on Centre Court.
The 25th seed will face the victor of the match that followed her on Centre Court between Germany's Tatjana Maria and France's Kristina Mladenovic.
"I got the practice that I needed", Wozniacki said.
"This time, I was playing against good player, so the pressure was little bit also on her side today. I don't know if third round, fourth round, but there is always a chance for me".
But what set her loss apart - more than the gritty slugfest of a match - was Wozniacki's unsporting response.
"For her to keep this level, I would be very surprised if you saw her go far".
Top 10-seeded winners Wednesday were No. 9 Venus Williams coming from a set down to beat Alexandra Dulgheru 4-6, 6-0, 6-1, and No. 10 Madison Keys beating Thailand's Luksika Kumkhum 6-4, 6-3. "I don't know if I've ever played her before, so it's always hard to play someone for the first time - I'm sure she's seen me play a lot".
Milos Raonic, the 2016 finalist, sits in Federer's half and blasted 34 aces in his 7-6 (7-4) 7-6 (7-4) 7-6 (7-4) victory over Australia's John Millman.
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