My employer stated that she would not allow me return to work because she thought I might be contagious. My doctor wrote a note stating that I was not suffering from an acute contagious condition. At the bottom she wrote call me with any questions. My employer did call her and was told that I was not released to return to work until I saw the pulmonologist I was referred to. She was also told that my illness had not been determined pending test results.
Did I give up my HIPAA rights by giving this note to my employer?

In a way, yes, but I don't believe HIPAA was actually broken because no "real" medical information was given by the doctor to your employer. Honestly, its hard to say without knowing specifics of what was talked about between your physician and employer.

My concern is why the doctor gave you a written excuse that doesn't seem to fit what was said over the phone.

No HIPAA violation and of course an employer has a right to know your condition and to expect a release from a doctor, on the phone or in writing, and I see no contradictions, only a little need for clarification.

Doctors and employers are afraid of liability, so expect to wait for the specialist.
I assume you have some sort of chronic cough or wheeze, and your fellow workers don't need to catch whatever it might be, right?
PS: I and some family all used to suffer from chronic coughs that would become bacterial infections after a month and I think we have stopped them with lots of home attention to lots of liquids, humidity, and fresh ginger and garlic. Better than 1 antibiotic after another.

No you did not give up your rights under HIPAA by handing the note over. However, your doctor has violated some tenants of his profession which may or may not constitute HIPAA violation but one of enthics. The note and the phone call are not in agreement. If you are upset by what happened report it to
Office of Civil Rights in the area in which the violation occurred. You may also email your complaint to [email protected].
. I am quoting the HIPAA privacy part here "Providers must obtain a patient's consent for the disclosure or use of the patient's health information" You did not sign off your rights so the doctor should not have said one word about your health other than what was written on the note.

OP may have signed such a release without remembering it.
Test results (radiologist reading X-rays for example) may have come in after the note was written and before OP saw the specialist.
Of many tens of thousands of HIPAA complaints, not one was found to be a violation.
Many employees think they can refuse to reveal conditions that are keeping them out sick, or refuse to comply when an employer says 'go home and don't come back without a note from a doctor.'
I doubt that any ethics violation occurred here either.

Used to be true but no longer Californian Sentenced to Prison for HIPAA Violation | Journal of AHIMA (http://journal.ahima.org/2010/04/29/californian-sentenced-to-prison-for-hipaa-violation/) RE: ethic, consider what the OP says was in the note and then what was said to the employer. Of course we are only seeing one side of this issue and I am sure the doctor would give reasons for saying or doingother than was in the note.

Interesting article.
Poor guy. I read an article once about privacy in China, where it was and in many areas still is practically routine for say, a president of a bank to publicly reveal financial information about customers, and for some reason this is accepted custom. I can believe that he didn't know anything about HIPAA. Ironic that the press gets to publish the names of celebrities whose files he looked at.
I should have figured that the report that HIPAA has never had a viable complaint would sooner or later be busted.

Nothing is forever, especially if Congress has had anything to do with it.