The reigning Spanish champion was one of the last riders to start his final lap and availed of the best of the conditions to claim the top spot. Sandro Cortese was just 0.012s behind Rins but ultimately it was the rookie who claimed the spoils.
The 16 year old will be joined on the front row by his teammate, Miguel Oliviera, after the Portuguese rider failed to claim the pole position after setting the pace throughout the wet practice sessions.
With conditions improving enormously in the closing minutes the session became a lottery but ultimately it was Rins who cashed the winning ticket.
With the Estrella Galicia squad claiming two starters on the front row the second row sees Caretta Technology teammates Alex Masbout and Jack Miller line up alongside one another with Jakub Kornfeil between them in fifth.
The Czech rider was one of the first to venture onto slick tyres and set the pace with only a couple of minutes remaining but he has given himself a fighting chance of a strong race tomorrow after his brave decision gave him more knowledge of the conditions than his rivals.
Issac Vinales will line up seventh after setting his time on slick tyres. His cousin, championship leader Maverick Vinales, was not so lucky. The Spaniard remained on wet weather tyres and had to settle for the ninth fastest time just ahead of Romano Fenati.
Arthur Sissis set the pace in the closing stages but the Australian ended the afternoon eighth and with Alex Marquez 13th fastest it was successful day for quite a few Grand Prix rookies.
Ultimately none of them would have as much reason to smile as Rins but with difficult conditions and mixed up grid there is potential for a tremendous race tomorrow.