The Belgian, champion in 2003, needed just 50 minutes to claim her place in the last 16, where she will play 15th seed Dinara Safina of Russia who defeated American wildcard Ahsha Rolle 6-4, 6-3.
Makarova had beaten Japanese 28th seed Ai Sugiyama in the previous round but world number one Henin was in a different class, allowing the Russian just eight points in the first set.
The world number 156 held serve in the fourth game of the second set and broke Henin in the seventh but the Belgian broke straight back to claim victory.
Meanwhile,  Maria Sharapova needed only 51 minutes to overwhelm Australian Casey Dellacqua in the second round serving notice that she is focused, in-form and determined to defend her title.
    The second-seeded Sharapova blasted 30 winners while yielding only two to her opponent during a 6-1, 6-0 rout under the lights at Arthur Ashe Stadium.
"I'm just trying to play solid from the first point until the end," said Sharapova, one of 10 Russian women in the third round. "I don't want to give my opponents any chances.
Most of the favourites breezed through on a sunny day and a cool evening at the National Tennis Center in Flushing Meadows.
16th seed Martina Hingis sliced, lobbed and chipped her way to a 6-2, 7-5 win over Pauline Parmentier of France while fourth seed Svetlana Kuznetsova employed power tennis in a 6-3, 4-6, 6-0 victory over Camille Pin.
Birthday boy
On the men's side, fifth seed Andy Roddick celebrated his 25th birthday with a second-round victory over Argentine Jose Acasuso, who retired with a knee injury at the end of the third set. Roddick, the 2003 champion, said he was just glad to advance.
"It's not the way you want to get through but at the beginning of the day all you want to do is get through to the third round," admitted the American, who was leading 4-6, 6-1, 6-2 when Acasuso left the court.  Other winners included fourth seed Nikolay Davydenko of Russia, ninth seed Tomas Berdych of the Czech Republic and Britain's number 19 Andy Murray.
Blake prevails
Sixth-seeded American James Blake outlasted cramping 34-year-old Fabrice Santoro of France in a tension-filled five-setter.
Blake, who had been 0-9 in five-set matches including three defeats in the U.S. Open, ripped a backhand, crosscourt winner to claim the three-hour, 25-minute match 6-4, 3-6, 6-2, 4-6, 6-4.
Santoro twice needed to have his legs massaged during changeovers and received a medical timeout during the sixth game of the final set for further treatment but gamely battled on.
Clutching his left thigh and back of his leg, Santoro went toe-to-toe with Blake to keep the final set on serve. The Frenchman held three breakpoints in the ninth game before Blake finally held for 5-4.
Santoro won the first two points in the 10th game but lost the next four, watching Blake's backhand winner whiz by to end the match. Both players received ovations from the Arthur Ashe Stadium crowd as they embraced at the net after their marathon match.
"He said, 'It's amazing what I'm doing at my age,'" recounted Santoro. "I said, 'Thank you, my son.'"