The Parkalgar Honda rider, fifth in the world championship standings, was promised more engine power by his team during the week, and the Lincolnshire based team have delivered.
This extra speed has also benefitted Jones' team mate, Portugese Miguiel Praia. He managed to get a little higher up the grid to 16th, though some way behind the times set by Jones and pole man Broc Parkes.
Jones finished fourth in the session, half a second off pole and just a shade slower than fellow Brit Jonathan Rea on the all conquering Ten Kate Honda.
"We had two good sessions today and I've got a good feel for the bike," said Jones.
"We made some gearing changes today that have given us some useful data and I am riding comfortably while not having to bite the screen to get a lap time, which is good.
Praia, a former Superbiike rider is gradually getting used to Supersport and bringing his times down. He completed the session just over one and a half seconds from pole.
"I am enjoying my riding right now," he said. "16th place is OK but I wish it could be better. I hope I can improve tomorrow."
Team manager Simon Buckmaster a privateer Grand Prix 500cc rider of note in the 80s is satisfied with the days result.
"We are in a good position thanks to all the effort put in at the workshop during the week. It's been a good day at the office," he said.
