Edit 1: New answer following emphasis from your hints
You are a:
Doctor
The one I obey, my dear commander
Keep on running I will not slander
For I know you will follow my lead
Call me in if you are in need
The one talking is the Doctor. The doctor listens to patients and do what they tell him to. (*cough I'm sick write me a prescription) The doctor told this guy not to run but he didn't listen. The doctor knows though that this guy will eventually follow his lead and asks him to request a house call when he needs a doctor. (Because the foolish guy kept running)
If one commands the other will follow
That's the deal, one has to swallow
Either way, I rely on you
We kiss goodnight and start anew
A doctor needs a good reputation and income so he is just as reliant on patients as patients are reliant on him. (With patients often having to swallow medication) Sometimes though you don't have to take medication but undergo surgery, in which case you "sleep" and start anew, either in the afterlife from a mistake (doctors are only human), or perhaps a new life of healthiness.
Mighty Dictator of all places
followed by all human races
Watch over all the new born lives
earn the fruit of fertile strifes
The letters MD are capitalized, meaning medical doctor. All human races rely on doctors. Doctors deliver all babies (anyone who delivers a baby and is not officially a doctor may as well be considered a doctor from that point on, that's tough stuff). All fertile strifes result in injuries (fights), and doctors are the ones who benefit from them (from all the business).
Endless love, you never disclaim
nor would you repel and never blame
Unbribable Protector, punish me
and I will follow tacitly
Doctors never say they love you, nor do they repel or blame patients (with the exception of Dr. House). Your lives are in their hands, they don't really take bribes because most of em have more than enough money, and if they don't like you then it's possible a 'mistake' can happen while under the knife.
The sands of life are running out... You shouldn't have pissed off the doctor.
The answer I'm thinking of "fits" but probably not what you're looking for.
The Heart
The one I obey, my dear commander
Keep on running I will not slander
For I know you will follow my lead
Call me in if you are in need
You follow your heart, sometimes you need to help it medically.
If one commands the other will follow
That's the deal, one has to swallow
Either way, I rely on you
We kiss goodnight and start anew
You rely on your heart, and are with it every night.
Mighty Dictator of all places
followed by all human races
Watch over all the new born lives
earn the fruit of fertile strifes
All human races have hearts; all newborns have one; fertile strifes represent troubles which ties in to "troubled heart"
Endless love, you never disclaim
nor would you repel and never blame
Unbribable Protector, punish me
and I will follow tacitly
Endless love could refer to forever beating heart, unbribable and can punish you with a heart attack
Again, probably not what you're looking for because it doesn't fit perfectly, but just barely enough to post.