Davies led from the start to build up a big lead to get his fifth career win.
He last won a WorldSBK race at the Nurburgring in Germany in 2013. Ducati last won a World Superbike race in 2012.
In the end Davies was a full three seconds clear of Race 1 winner Jonathan Rea, who held off Leon Haslam for his sixth straight top-two finish.
Jordi Torres scored fourth place ahead of countryman Xavi Fores. David Salom won out in a dramatic five-way battle for sixth.
Kawasaki rider Tom Sykes was unable to finish the race after falling off his bike on lap 6 of the race when he was in fourth place.
Honda's reigning champion Sylvain Guintoli also fell at the fast turn 14 but was able to walk away uninjured like Sykes earlier.
Alex Lowes, riding a Suzuki, also ran off the track early but recovered somewhat to salvage two points with 14th position at the end.
Race 2 results at the Motorland Aragon circuit in Spain:
1. Chaz Davies GBR Aruba.it Racing Ducati 1199R 18 laps
2. Jonathan Rea GBR Kawasaki Racing ZX-10R 3.190s
3. Leon Haslam GBR Red Devils Roma Aprilia RSV4 3.712s
4. Jordi Torres ESP Red Devils Roma Aprilia RSV4 14.216s
5. Xavi Fores ESP Aruba.it Racing Ducati 1199R 20.524s
6. David Salom ESP Pedercini Kawasaki ZX-10R 25.878s
7. Leandro Mercado ARG Barni Ducati 1199R 25.939s
8. Michael van der Mark NED PATA Honda CBR1000RR 26.075s
9. Ayrton Badovini ITA BMW Italia S1000RR 27.253s
10. Nico Terol ESP Althea Ducati 1199R 28.666s
11. Matteo Baiocco ITA Althea Ducati 1199R 41.083s
12. Roman Ramos ESP GO Eleven Kawasaki ZX-10R 41.983s
13. Randy de Puniet FRA Voltcom Crescent Suzuki GSX-R1000 42.961s
14. Alex Lowes GBR Voltcom Crescent Suzuki GSX-R1000 43.057s
15. Leon Camier GBR MV Agusta F4 RR 43.375s
16. Christophe Ponsson LUX Grillini Kawasaki ZX-10R 59.193s
17. Santiago Barragan ESP Grillini Kawasaki ZX-10R 59.296s
18. Niccolo Canepa ITA Team Hero EBR 1190RX 76.004s
19. Larry Pegram USA Team Hero EBR 1190RX 93.714s
20. Imre Toth HUN Team Toth BMW S1000RR 1 lap
Javier Alviz ESP Pedercini Kawasaki ZX-10R 11 laps
Sylvain Guintoli FRA PATA Honda CBR1000RR 13 laps
Tom Sykes GBR Kawasaki Racing ZX-10R
Gabor Rizmayer HUN Team Toth BMW S1000RR did not start