Ramires volleyed in on 50 minutes and Cesc Fabregas hit the winner with a fine individual goal 10 minutes from time.
Ramires grabbed the winner after Fernando Torres opened the scoring for the blues in a 2-1 victory.
Van Ginkel was replaced by Ramires, who in the 35th minute added to Fernando Torres's opening goal. But Ramires too also failed to complete the match, going off at half-time.
Ramires and Bernard shone in midfield having been drafted into Scolari's starting lineup after injuries to Hulk (hamstring) and Oscar (ankle) during the week.
Jo bagged a double while Neymar, Ramires, Pato and Luiz Gustavo also netted a goal each to equal Brazil's highest score against Australia from the 1997 Confederations Cup final.
Spain's Fernando Torres' early strike had been cancelled out by Franck Ribery's second-half thunderbolt while Chelsea's Ramires was dismissed in the 85th minute as it finished 1-1 after 90 minutes at Prague's Eden Arena. Eden Hazard looked to have hit an extra-time winner for Jose Mourinho's Europa League winners before Javi Martinez's 121st-minute equaliser.
Two belters from Ramires and another brace from Romelu Lukaku swelled the Chelsea scoreline, as Indonesia's lone score came from a late Tomas Kalas own goal. Hazard got the opener with a penalty, captain John Terry nodded a trademark header, Bertrand Traore scored a beauty and Demba Ba was also on the scoresheet.
England midfielder Frank Lampard said that new Barcelona signing Neymar has the potential to be as good as Lionel Messi and Cristiano Ronaldo.
Christian Benteke put Villa ahead in the first half but, with both sides reduced to 10 men, Lampard started Chelsea's comeback in the 61st minute.
The result will also complicate Benitez's preparations for next week's Europa League final against Benfica, but it did allow Spurs manager Andre Villas-Boas to depart with a smile after his first game back at Stamford Bridge since he was sacked by Chelsea last year.