In a carbon copy of stage five of the 2012 edition - eight city circuit loops of Logroño also won by Degenkolb - the Giant-Shimano rider proved the strongest in a select group of sprinters that had avoided a mass pile-up on the final bend of the 166km stage.
With double stage winner Nacer Bouhanni (FDJ) and Australian Michael Matthews (Orica-GreenEdge) among those caught up by the incident, Degenkolb profited from a perfect lead-out by Dutch team-mate Ramon Sinkeldam before crossing the line ahead of the bearded Boonen.
Italy's Jacopo Guarnieri (Astana) took third place ahead of a resurgent Peter Sagan (Cannondale) and Max Richeze (Lampre-Merida).
Victory saw Degenkolb increase his tally to 112 points in the green jersey competition, with nearest rival Bouhanni on 78.
Spain's Alberto Contador (Tinkoff-Saxo) kept out of trouble to retain his 20-second lead over compatriot Alejandro Valverde (Movistar) in the overall standings. Colombian Rigoberto Uran (Omega Pharma-Quick Step) is third at 1:08 and Britain's Chris Froome (Team Sky) is fourth place at 1:20.
ONE-MAN BREAK: With a bunch sprint pretty much guaranteed it was always going to take a brave soul to try and defy the rules of logic. It was left to Matthias Krizek of Cannondale to do the honours, the Austrian breaking away on the first of eight sleepy circuit to build up a maximum lead of eight minutes over the peloton.
Krizek cut a lonely figure as the pursuing peloton edged around Logroño at a low average speed of 34kmph for the first few hours of soft-pedal racing. The 26-year-old Grand Tour debutant was eventually swept up with 12km remaining as the Tinkoff-Saxo team of race leader Contador rode a fast tempo on the front to protect their man in red.
SIESTA TO FIESTA: The stage finally sprung into life inside the closing kilometres as Manuel Quinziato (BMC) went for a long-range attack with 2.5km remaining. The veteran Italian lead the streamlined peloton into a tricky right-hand bend with 2km remaining before easing up as the main sprinters started to show their cards.
Italy's Roberto Ferrari launched his final sprint extremely early, jumping clear with Belorussian Yauheni Hutarovich (Ag2R-La Mondiale) on his back wheel just after the kilometre-to-go banner. The move could well have been in response to the carnage behind as over a dozen riders hit the deck to hold up the majority of the peloton - including Bouhanni, Matthews, Italy's Andrea Guardini (Astana) and Germany's Gerald Ciolek (MTN-Qhubeka).
Boonen - whose last Grand Tour stage win came in the 2008 Vuelta - powered through but was reeled in by Degenkolb after an expert lead-out by Sinkeldam.
Young Belgian sprinter Jasper Stuyven was in the mix - and had Trek Factory Racing team-mate Fabian Cancellara in support - but the 22-year-old could only finish in the Swiss powerhouse's back wheel for ninth place.
Frenchmen Yannick Martinez (Europcar) and Lloyd Mondory (Ag2R-La Mondiale) were sixth and seventh, while Hutarovich and Ferrari faded to finish eleventh and fourteenth respectively.
Giant's German cyclist John Degenkolb (C) celebrates his victory on the podium of the 12nd stage of the 69th edition …
RIDE OF THE DAY: It could be churlish not to give the award to John Degenkolb - particularly as his third win of the race strengthened his lead in the green jersey points competition - but a big 'chapeau' must go to Matthias Krizek, for so long the lone leader of the stage. The Austrian's move was crazy - but someone had to do it or we may not have had a race at all.
DAY TO FORGET: Any of the sprinters who were caught up by that incident in the closing kilometres - and Nacer Bouhanni in particular. The Frenchman had picked up points at the intermediate sprints only to see his hopes dashed in the finale. In a mountains-heavy final 10 days, there won't be many more chances for the sprinters to add to their tally of points or stage scalps.
COMING UP: Friday's 189km stage 13 is ideally suited for a breakaway with a long flat opening half followed by three lower category climbs and then 5% ramp to the finish in Obregon.
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- Nacer Bouhanni
- Matthias Krizek