49-year-old Ahlquist, who has three Paralympic medals, was without a chance and lost with a clear 11-4,11-9,11-9.
She came to Tokyo as a big medal jumper.
A victory in the quarterfinals had secured a medal because no bronze match is played.
Ahlquist had no weapons to use against the Slovak, who was tight and did not drop anything, constantly finding intangible angles.
Ahlquist completed a rare heavy Swedish day in the ping pong garden, where all four Swedes who were in the round of 16 or quarterfinals lost their matches.
- It is incredibly painful and four heavy losses for Sweden.
Now we have to recharge for the team game, says Ahlquist wearing a mouth guard with tears in his eyes.
- It is very heavy and I need time to digest this, she says from her wheelchair.
On Sunday, the team competition begins where Ahlquist plays with Ingela Lundbäck.