Meanwhile, Newport's Tom Booth-Amos recovered from a crash in race one to bag another win in World Supersport 300 to keep up his title aspirations.
Mid Wales star Davies began the weekend struggling with the front end of his Ducati during free practice at the famous Dutch circuit and caught debris in his rear tyre, which damaged both the swingarm and tyre during qualifying.
Lining up 13th on the grid for race one, the 34-year-old recovered to take ninth at the chequered flag.
Davies knew his goal for Sunday's points-scoring Superpole was to at the very least finish in the top nine, to secure a decent grid position for the main race.
And despite the threat of rain he did just that, finishing ninth for the second race running.
Davies headed into race two full of confidence and after a great start he managed to overtake Tom Sykes, Alex Lowes and went in pursuit of Scott Redding and Michael Rinaldi for third place.
As Redding pulled away and eventually finished second, Davies and Rinaldi continued their battle, which eventually saw the Team Go Eleven rider take fourth position as he defended a late challenge from former team-mate Alvaro Bautista.
Davies said: "We made a quite big change on the bike and it was good.
"It was turning much more naturally and that helped not only the performance of the bike, but also from a physical point of view.
"I could let the bike do the work naturally, so credit to my crew for making a step forward, for being brave.
"Unfortunately, we then suffered the same problem as on Saturday because, with seven laps to go, I killed the front tyre.
"That was a bit disappointing because I was really feeling like I could get in the mix for the podium, catching Scott a little bit.
"The rear tyre was quite good but the front was absolutely dead.
"I was the top independent, so I was happy with that and thanks to Team Go Eleven."
Booth-Amos was also back on the world stage having kept busy during the break racing in the British Junior Supersport series and also at Goodwood.
The 24-year-old was in contention for a podium for most of the race but crashed out in the final corner and was forced to retire.
Further bad luck arrived when he received a grid penalty of nine places for race two for "riding in a slow manner" during Saturday’s Superpole.
Despite all the the setbacks, the RT Motorsports by SKM rider managed to take the lead and then broke away from the chasing pack on the last corner to claim another win, which keeps him second in the championship standings.
Team boss Rob Vennegoor: “I’m so happy for Tom and our team after his crashes at Misano and Assen.
"He did a superb job after the grid penalty and stayed focused despite all the bad luck he had before race two.
"It is very positive we ended on the podium.
"I would like to thank all riders, team members and sponsors again as everybody has worked so hard this weekend. It’s wonderful to be part of this team.’