The Integro Yamaha rider beat GP2 front-runner Kyle Ryde by almost three tenths of a second, while his Appleyard team-mate Brad Jones settled for third - almost a second off the top spot.
Dubliner Kennedy controlled the entire session from lights-to-flag with Jones and title rival Alastair Seeley slotting in behind to round out the provisional front row with just over half the session completed.
But with just a few minutes to go, RS Racing Kalex man Ryde powered into second place just as SGR Racing's Tom Oliver and ABM Quattro Triumph rider Mason Law jumped ahead of Seeley.
No one could top Kennedy, however, who clinched yet another pole position, set to start alongside Ryde and Jones on the front row of today's Sprint race grid.
Oliver will lead off row two ahead of Law and EHA Racing's former champ Seeley.