The 43-year-old arrived at Meadow Lane in February 2012 as development squad manager, and was then appointed first-team boss following the departure of Keith Curle one year later.
However, Notts have only won two of 13 league matches this season, and a 1-0 defeat to Preston North End proved to be Kiwomya's last game as Magpies boss, and one loss too many for the club's board.
"I cannot express how difficult a decision this has been for the Board of Directors," chief executive Jim Rodwell told the club's official website. "This has been a gruelling year for Chris, both on the pitch and personally. Chris has conducted himself with dignity and professionalism throughout.
"We would like to state, for the record, that we continue to hold Chris in high regard. His work rate, enthusiasm, commitment to the club and, importantly, honesty and integrity are commodities rare in football today.
"We put our faith in Chris towards the end of last season and genuinely thought that we had found the man to bring stability and a long-term vision to the manager's role here at Notts. However, it simply hasn't worked out how we had envisaged and unfortunately, as we all know, this is a results driven business."
Steve Hodge, who was Kiwomya's replacement as development squad boss, has been put in temporary charge, with Notts next in action against Oldham Athletic on Tuesday.