Aces lost 2-0 to Kaizer Chiefs in their last match of the year on Wednesday night.
The club said the decision came after lengthy meetings where all matters and issues were discussed in depth and both parties agreed to shake hands amicably and try for a different solution.
"Neil Tovey is an absolute professional and he brought a whole new level of thinking, structures and training to the club. However, things were just not working out as planned and both parties agreed it made more sense at present to move in different directions," said the statement on the club's website.
The Mpumalanga-based club CEO Marc Grune praised Tovey for bringing in a fresh approach and more professional leadership to Aces.
"It was an eye-opener in terms of new ideas and structures. I enjoyed working with Neil and his total professionalism. He has done great things for the sport as a player and we all admire him for that. As a coach he brings his own style of South African play to the field and the players responded well to that initially"
"It has been really unfortunate that results were then not forthcoming as he worked incredibly hard for that. The players must shoulder a big part of that responsibility too, but it was clear that at this present time the fit was just not there. It is a real pity and we are very disappointed," concluded Grune.
The club further mentioned that they will not make further comments and asked the media and supporters to "understand this move as being in the best interest of both parties".