Henman, seeded sixth, appears to have lost a little confidence since his first-round defeat by Germany's Martin Sinner in the Dubai Open last week. His backhand repeatedly let him down yesterday.
Bruguera, a wild-card entry, is ranked 47 in the world, 28 places below Henman, but he is still a class player, having twice won the French Open, in 1993 and 1994.
The British No 1 took the first set easily enough and was twice a break up in the second before Bruguera squared the match at one set all. Then, in a third set of missed chances on both sides, games went with serve to 4-4, before Henman gained the only break in the ninth game to lead 5-4 and served out for victory.
Reaching the final of the Qatar Open in Doha and then winning the Sydney International last month took Henman up to 14 in the world rankings.
Since then he has lost in the third round of the Australian Open and the first round in Dubai and is now down to 19.
He has also been struggling slightly with a groin injury, a legacy of too much physical work in the past few weeks as he tries to build up his strength.
"I wasn't able to finish the job off and that's where I probably made life difficult for myself,'' Henman said. "I was able to hang in there and got my opportunity in the third and was able to hang on to it. I'm pleased to come through a match like that. I needed it."
Henman, 22, now meets Mikael Tillstrom in the second round in what will be his first match with the Swedish player.
Ivanisevic withdrew with tendinitis in his shoulder, only hours after Boris Becker pulled out because of tendinitis in his wrist.
Ivanisevic, a former winner in Antwerp, was beaten by the Austrian Thomas Muster in the final of the Dubai Open on Sunday. He was due to play Guy Forget, of France, in a first-round match today.
In another first-round match, the defending champion, Michael Stich, who was furious over some disputed line calls, fell to a 7-6, 6-4 defeat by his fellow German Marc-Kevin Goellner yesterday. Stich, beaten in the first round of last week's Marseilles Open, called for the ATP supervisor midway through the second set but his pleas to have a linesman changed were refused.
n The British No 2, Greg Rusedski, has pulled out of the ATP Tour event in Memphis because of wrist trouble. The 23-year-old, who hurt his left wrist in Sunday's final in San Jose - which he conceded - against the world No 1, Pete Sampras, saw a Los Angeles specialist yesterday and was advised to withdraw.