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.
Lampard claimed his 201st Chelsea goal from the penalty spot to secure a 2-0 victory over Swansea at Stamford Bridge on Sunday after appearing as a 24th minute replacement for the injured Ramires.
United had appeared to be cruising into the semi-finals after early goals from Javier Hernandez and the recalled Wayne Rooney put them in control on a wintry afternoon at Old Trafford. Their poise disappeared in the second half though, as goals from Eden Hazard and Ramires brought Chelsea back into the tie, and Ferguson said Tuesday's sapping Champions League loss...
Eden Hazard came off the bench to give Chelsea a lifeline with a fine finish in the 59th minute and Brazil midfielder Ramires slotted home the equaliser nine minutes later to set up a replay at Stamford Bridge.
Interim manager Rafael Benitez has complained about fixture congestion in recent weeks, but with his side also still in contention in the Europa League, the European champions look set for a busy few weeks.
Lampard, who scored England's match-winner against Brazil on Wednesday, got his 12th Chelsea goal of the season.
Wilshere hobbled off following a strong challenge from Alfred N'Diaye and Arsenal were reduced to 10 men when right-back Carl Jenkinson was dismissed for a second booking after fouling Stephane Sessegnon in the 62nd minute.
Real Madrid star Kaka and Chelsea trio David Luiz, Ramires and Oscar figure in the squad released Wednesday for Brazil's 1000th game, a friendly against Colombia in the United States.
The global football players' union says UEFA has rejected its appeal for six suspended Bayern Munich and Chelsea players to be allowed to play in the Champions League final.