Mixed weather conditions made the superb Sevlievo circuit a slippery challenge, with Barragan the last of its many victims during an exciting day of racing in both classes.
The AXO KTM rider had finished second to Philippaerts in race one and so looked set to not only win the second race, but also take the overall, when his 450 suddenly kicked sideways over a jump - spitting the Spaniard over the handlebars upon landing.
Barragan sprang to his feet, but both Sebastien Pourcel and Philippaerts were able to get ahead - with world champion Steve Ramon demoting a devastated Barragan to fourth place by the flag.
Philippaerts thus took overall victory for Monster Yamaha, with Barragan salvaging second ahead of pole sitter Pourcel, whose overall victory hopes were damaged by a eighth in moto one.
Philippaerts now holds a 17 point lead over Suzuki star Ramon (5-3 on Sunday) in the championship standings, with Josh Coppins a further 17 points back in third after 4-7 moto finishes.
The MX2 podium was dominated by KTM riders, after Yamaha's world champion Antonio Cairoli - who took victory in moto one - suffered a 'character building' second moto.
Cairoli had exchanged the lead with Tommy Searle several times on his way to a 2.9secs victory margin over the Englishman in race one, with Searle's Red Bull KTM team-mate and fellow title contender Tyla Rattray third.
But Toni fell moments after taking the holeshot at the start of moto two - and was hit by Rattray - leaving Cairoli dead last. Searle escaped the carnage to slot into second behind fellow Brit - and KTM rider - Shaun Simpson, who successfully held off the 2007 world championship runner-up until the very last lap.
Third place behind Searle and Simpson went to Nicolas Aubin, with Rattray recovering to fifth, but Cairoli struggled to start his machine after a second accident and could only manage 19th at the flag.
The overall podium this consisted of Searle, Rattray and Simpson, with Rattray now back ahead of Cairoli by four points in the world championship standings - and Searle only four points behind the Italian ace in third.
Cairoli's home event, the Grand Prix of Italy, takes place next weekend.