In the last game of the day, Russian third seed Svetlana Kutznestsova also struggled before outlasting Katarina Srebotnik of Slovenia, ranked 23rd in the world, 6-7, 6-4, 7-6 (4) in two hours and 31 minutes.
Top seed Henin, who had played her last competitive match when she won last year's season-ending WTA Tour championships in Madrid on Nov. 12, won 3-6, 6-2, 6-2 in 82 minutes.
"It's never easy to return to competition. I always have problems. In the first set, I didn't play very well but I was expecting it, then I found a better rhythm," the Belgian said.
Henin, who lost her world number one spot to Maria Sharapova after skipping the Australian Open following a split from her husband, will face Tatiana Golovin or Russian qualifier Ekaterina Bychkova in the quarter-finals.
Golovin defeated fellow Frenchwoman Alize Cornet 6-2, 6-2 on Wednesday. Bychkova ousted sixth seed Patty Schnyder of Switzerland on Tuesday.
Also on Wednesday, Camille Pin, ranked number 75 in the world, came close to upsetting Russian seventh seed Dinara Safina, winner of the tournament in 2005.
The diminutive French player served for the match but lost 2-6, 6-2, 7-6 in two hours and 13 minutes.
Russian eighth seed Anna Chakvetadze powered through to the second round with a 6-2, 6-0 demolition of compatriot Olga Poutchkova, winning 10 games in a row to wrap up her win in 52 minutes.
She will meet Anabel Medina Garrigues for a place in the quarter-finals after the Spaniard defeated Frenchwoman Severine Bremond 6-2, 7-5.