The German, who beat Serena Williams at the All England Club before losing to Marion Bartoli in the final, lost 6-4 7-5 to the big-hitting Russian at Flushing Meadows.
Lisicki, the 16th seed here, has reached the fourth round in New York just once but would have hoped to build on her great run in SW19.
Agnieszka Radwanska was another of Lisicki's victims at Wimbledon, and she had a tough outing against 32nd seed Anastasia Pavlyuchenkova but came through 6-4 7-6 (7/1).
The third seed, who faces Makarova next, has never been beyond the fourth round at Flushing Meadows.
She said: "I'm very happy that I won another match in two sets. Of course it was tough, two tight sets. It was just by a couple of points.
"But definitely I played very good in the tie-break. I was really focused from the beginning, and I just wanted to win the tie-break very much.
"Of course I will do everything to make the quarter-final this year.
"I like hard court and I really had great results on that surface. I think it's just something wrong here that I can't pass the fourth round. This is another opportunity, so I will try my best."
Sixth seed Li Na gained revenge on her 2012 conqueror Laura Robson with a 6-2 7-5 win in the opening match on Arthur Ashe.
The Chinesewoman was upset by teenager Robson at the same stage last year but played a high-quality match and recovered from 0-3 in the second set.
Li also served 11 aces, which took her by surprise.
The 31-year-old said: "I think this year I have improved a lot, especially on the serve and also coming to the net."
She admitted she felt nervous prior to the match but a chat with coach Carlos Rodriguez calmed her down.
"He said something to help me and to take the pressure off," she said. "After the talk I was feeling much, much better. Before I never tried to share this feeling with my team."