2-Pin Fan Connector – Identification Guide

I finally asked the right high reliability supplier. The connector was a custom from MinECon . The link below points to similar connectors. Hope this updated answer helps the one other person on Earth who is looking for this type of connector.

http://www.min-e-con.com/s_series.html

As @Nick Alexeev said in the comment, it's propably a Molex PicoBlade.

http://uk.farnell.com/molex/53261-0471/wire-board-connector-header-4pos/dp/2411457

Can't be sure only looking at your picture. If it would be me, I would get a plug that fits into your controller since you can see exactly what kind of connector you need from the controllers datsheet and replace the small connector from the fan. Soldering wires is not a bad thing either but wires have a habit of breaking off pretty easily. Hot glueing around the solder is a cheap man's trick thats not pretty but works.