Davies (Ducati) set a new qualifying record to claim Superpole at the MotorLand Aragon circuit and was on course to end Rea's winning run after holding off the Kawasaki rider for much of race one.
But the Welshman crashed out on the penultimate lap.
World champion Rea powers to first victory in Jerez
Rea crossed the line ahead of Marco Melandri (Ducati) and team-mate Tom Sykes to maintain his 100 per cent record in 2017.
The Northern Irishman is now 47 points clear of Sykes in his bid for a third successive title.
Jonathan Rea savours ‘incredible’ win
Alex Lowes finished fourth despite starting in the fourth row after his qualifying session was ended by a technical problem with his Yamaha.
His team-mate Michael van der Mark completed the top five with Spaniard Jordi Torres (BMW) taking sixth place in his home race.
Melandri fastest in final practice in Spain
Chaz Davies: 'Perfect end to a disastrous weekend'