Hoy, who claimed his fifth and sixth Olympic golds at London 2012, took to the track four points ahead of Kenny but was to come off it with his cushion narrowed down to three.
The 36-year-old started the evening with victory in the team sprint, this time with seven world champion Gregory Bauge as the pairings once again rotated and they beat Kenny and Teun Mulder.
However Kenny got the better of Hoy in the individual sprint, qualifying faster, before the triple Olympic champion beat Bauge in the semi-finals and Mulder in the major final.
Hoy lost to Mulder in the semi-finals but recovered to beat Bauge thereafter to claim third before winning from Kenny in the keirin as he edges closer to winning the Giant Sprint Masters title.
He leads the four-strong field with 29 points with Kenny three behind on 32 while Mulder and Bauge are a way off the British pair in third and fourth with 48 and 61 respectively.