Rea, meanwhile, held a comfortable margin over Leon Haslam, Spies, Checa and Max Biaggi, the Italian recovering from a few 'wide' moments early on to catch and pass Fabrizio and Troy Corser.
Whilst not as prolific as his progress in race one, Spies was still proving to be a race win contender as he shadowed Haslam in second place, the American eventually getting the better of him under braking at his favoured overtaking spot, the Esses.
Setting off in pursuit of Rea, Spies was able to catch the youngster, but was never close enough to launch anything more than the occasional lunge to unsettle him. Safe in the knowledge that he is the new championship leader, Spies pushed hard on the final lap, but had no answer to Rea, who shrugged off the pressure to not only keep Spies at bay, but also set a new lap record in the process.
Spies was forced to play second fiddle, but the result means he has turned a two point deficit into an 18 point advantage at a crucial stage in the season, with only six races remaining.
An error by Haslam shortly after Spies had overtaken him promoted Checa up to third position for his second podium of the day, the Spaniard completing an outstanding weekend for Ronald ten Kate's eponymous team.
Biaggi was another to benefit from a fading Haslam to secure another top five finish on an Aprilia that had threatened to be off the pace during the initial stages of the weekend. Haslam, meanwhile, held on for another solid result to consolidate his sixth place in the standings.
Although not quite as good as his fifth place finish in Brno, a sixth and an eighth for Troy Corser
signals his and BMW's best combined result of the season, the S1000RR beginning to prove it has the pace – if not the longevity – to challenge at the front of the field now.
Having barely featured all weekend, an inspired Ryuichi Kiyonari
was a surprising seventh after battling his way up from 18th on the grid and passing Tom Sykes and Fabrizio in the closing stages, the latter rider enduring a disappointing weekend to all but end his title hopes.
Suzuki were on for a possible double top ten finish, which would have been their first since Valencia, but an accident for Karl Muggeridge
put paid to that. He had been ahead of team-mate Yukio Kagayama
up to that point, but it was the Japanese rider who would inherit to snatch tenth position.
Jakub Smrz was eleventh on an unusually quiet day for him, while Fonsi Nieto, Broc Parkes, Luca Scassa and Vittorio Iannuzzo completed the points positions, the latter scoring his second point of the year.