The Magpies made a losing start to life without Keith Curle, who was sacked on Sunday.
Curle left following the 2-1 loss at bottom-club Hartlepool on Saturday, with development squad manager Kiwomya stepping in on a temporary basis.
But goals in the first and last minutes of normal time at the Lamex Stadium handed Kiwomya defeat in his first game at the helm.
After 25 seconds Sam Hoskins tapped into an empty net when Filipe Morais' shot was blocked and fell kindly to him, with Marcus Haber heading home unmarked in the final minute.
Kiwomya, though, felt his side had deserved better.
"There has been a lot of change within 24 hours but they gave me 100 per cent," he said. "We gave them an early goal which was bit of a setback but our reaction was excellent.
"We went in there, we put balls in the box and we put a lot of pressure on. They changed their system to stop us because they didn't want us coming through the middle.
"We just couldn't get that ball in the net which has been a problem for most of the season to tell the truth.
"I haven't been told how long I've got. They asked me to take it on and it was very much enjoyable. It's a good experience for me and the lads worked hard - I will keep going until told otherwise."