Henin has yet to impress in her first WTA tournament on home soil in five years. The Belgian has often looked edgy against average opponents this week and even twice trailed by a set.
It was the third match in a row Henin faced a qualifier, the 94th-ranked Bacsinszky, who led 3-0 after only nine minutes because of unforced errors.
"She has a lot of potential," Henin said of her 18-year-old opponent. "I knew it was going to be tough and it proved that way."
Henin immediately broke in the second set. In reply, Bacsinszky quickly earned five break points but this time Henin held on and started exploiting her opponent's weak forehand to even the match.
Henin won a love-game to start the deciding set and soon broke the struggling Swiss with increasingly dominant play to reach a 4-1 lead. Henin wasted three match points at 5-2, winning on the fourth attempt.
"She beat me but I did my best and fought all the way," said Bacsinszky, who survived a match point in the first round and advanced from the quarterfinals after third-ranked Daniela Hantuchova withdrew with breathing problems.
Knapp, ranked 47th in the world, beat Li by staying calm beyond the baseline while the Chinese committed unforced errors throughout the match.
Knapp, who had not won a match this year before arriving in Antwerp, beat fourth-seeded Patty Schnyder on her way to the final. Now comes the toughest challenge of all.
"It is great," Knapp said. "I can play against [Henin] for the first time in my career and I'm excited."