Sam Hoskins and substitute Marcus Haber scored in the first and final minutes of normal time on Tuesday night to condemn County to back-to-back defeats.
Kiwomya, in caretaker charge following Sunday's sacking of Keith Curle, got off to the worst possible start when the hosts took the lead after just 25 seconds.
A Filipe Morais shot took a deflection off Alan Sheehan and fell kindly to the feet of Hoskins, who rolled into a vacant net with County keeper Fabian Spiess grounded.
The visitors' response was immediate as Jeff Hughes slid home from close range - but he had already been flagged offside.
Yoann Arquin's volley cleared the stands and Hughes headed over as Notts enjoyed the better of the first half.
After the break dominant County saw Francois Zoko and Hughes fire wide but Haber leapt highest to head home and seal three points for Boro.