It is directing someone to a location near you. For your example of sitting with Ahmad and Ali, Ahmad is directing Ali to sit down in a spot near to Ahmad. When I do this, I usually gesture with my hand to the spot so it is clear where "over here" is referring to. Here is another example: Ahmad and Sara want a photograph taken. Sara wants Ahmad to stand next to her, so Sara says, "Ahmad, stand over here" as she points to the ground next to her. In both examples, just saying "here" instead of "over here" also works. "You can sit here" or "stand here" is okay.

Essentially, it means 'come and sit with us (in the place we are currently sat)'. Because in the example you give, Sara and Ahmad are sat in one place and Ali in a different place and Sara and Ahmad want Ali to come sit with them. Hence, they say over here (with us).