I have a car loan that is pretty low interest at 3.49%. It has 3k left and I have enough to take it out and still have an emergency fund for rent, and the small student loans I still have. Each month I pay $450 on the car so it has 7 payments left on it. Since the emergency fund should secure all purchases you need for the next 3-6 months, and in the event of being out of work and needing the emergency fund I would have to continue paying the car payment (or sell it). Therefore should you use the emergency fund once the amount of time you're preparing for with the emergency fund is the same as a car loan?
In this case, it likely makes very little difference, assuming you have your emergency fund earning ~2% interest the difference between paying your car loan off now or monthly over 7 months is just a few dollars. Are you comfortable reducing your emergency fund by $3k now to save a bit of interest? If you lost your job tomorrow would that $3k reduction stress you out? I assume there's no early payment penalty on your car loan, but that would also impact your decision.
If you choose to pay now, I'd suggest rebuilding your emergency fund to the same level in anticipation of car repairs (unless you are already budgeting and saving separately for those). Similarly if you just keep making the monthly car payments don't reduce the amount in your emergency fund when the car is paid off.
3-6 months is a fine guideline for an emergency fund, but many people are more comfortable with 6-8 months. Just try to think through all the costs of unemployment and how long it might take you to find a comparable job to help decide how much emergency fund is right for you.
I think you can safely pay it off. From your comment I see your emergency fund can cover 6 months of bills, and one of those bills is a car loan that you would no longer need to include in your emergency fund if you paid it off, so once you have 6 months or less remaining, then paying it off is mathematically correct if your interest rate is greater than 0%. To be exact you could wait one more month until you have 6 months remaining instead of 7, however, since emergency fund amounts are somewhat arbitrary anyway, if you're comfortable with it I'd just pay it off and be done with it. I calculate you'll save approximately $35 in interest if you pay it off now.