The two KTM Ajo riders had been outside the top 20 after both of Friday's practice sessions were run in wet conditions, but booked their places in Qualifying 2 when the track dried out for Free Practice 3.
The return of rain midway through Qualifying 1 created uncertainty again, but it cleared in time for the second 15-minute stanza which decides the pointy end of the starting grid.
Aron Canet (Inde Aspar) was the early pace-setter in the latter session on a 1:38.272s, and fastest again by the time the second flyers were done, on a 1:37.033s.
Gardner, who was part of a Moto3-style track position game as the field set off for Q2, jumped from 14th to the top with a 1:36.861s on his third full lap of the Misano World Circuit Marco Simoncelli.
Jorge Navarro (+Ego Speed Up) beat the latter with a 1:36.928s but Canet was back onto the front row with a 1:36.869s moments later, after which he needed his elbow to save his front end from folding completely at Turn 3.
Augusto Fernandez went from seventh to second with a 1:36.788s in the final minute before the chequered flag, and Lowes consolidated provisional pole with a 1:36.615s.
However, that was nowhere near enough to hold onto it, as Raul Fernandez would subsequently charge to a 1:36.264s and take his fifth pole position of his rookie season.
Gardner's 1:36.861s left him fourth, with Canet next to the Australian and Navarro also making it onto Row 2.
The 25-lap Moto2 race is due to start on Sunday at 20:20 AEST.