On Tuesday (9/2) I had my upper left wisdom tooth removed. The next day I finished the amoxocillian that was prescribed the Thursday before when I started having symptoms. On Thursday in the morning I woke up feeling sluggish, with body pain and chills. Since Thursday (four days) I have been running a fever. Do you think this is related to the tooth extraction or am I just sick?

It could just be coincidence but the surgical site could be infected. Have your dentist take a look, you may need another about of antibiotics. I trust you are rinsing gently with warm water and salt to help promote healing.

Usually an infection will also have a bad taste/odor, and swelling/pain from the site.. also limited opening of the jaw

Fever is also related to infection.