Dokic lost her first match back after winning in Tokyo
Third seed Dokic served for a place in the last eight in the second set but eventually went down 4-6 7-6 (8/6) 6-0 to Hantuchova, a qualifier.
Dokic received a bye in the first round and was playing in her first match since winning the Toyota Princess Cup in Tokyo last Sunday.
The Yugoslav was on the verge of victory at 6-5 ahead in the second set, but Hantuchova broke to love and then took the tie-break when Dokic double faulted.
The Slovakian dominated the final set and took the match with two successive aces.
"I was thinking all the time I could win the match but I knew I had to improve after the first set," said Hantuchova.
"I was very aggressive and didn't let her play her game."
Hantuchova will meet seventh seeded Russian Elena Dementieva in the quarter-finals.
Anna out
Top seed and defending champion Kim Clijsters of Belgium had a comfortable 6-3 6-3 win over Italy's Francesca Schiavone.
Clijsters meets another Italian, fifth seed Silvia Farina Elia, in the last eight.
Anna Kournikova, meanwhile, suffered defeat at the hands of fellow Russian Anastasia Myskina.
Myskina, a 'lucky loser' restored to the main draw after the withdrawals of Serena Williams and other high-ranked players, prevailed 6-4 3-6 6-3.
"I wanted to win but the important thing for me is that I have no problems with my foot in the next few weeks," said Kournikova afterwards.
"Then I'll be able to play better tennis soon."