World Cup semifinalists Portugal were the other big name to go down when they lost 2-1 away to a revitalised Poland, who continued the honeymoon period for Dutchman Leo Beenhakker.
Otherwise, the evening went to form as Italy won their second successive game with a 3-1 win in Georgia, Germany crushed Slovakia 4-1 in Bratislavia and World Cup finalists France cruised to a 5-0 victory over Faroe Islands.
Scotland's dream run hit a minor hurdle when they lost 2-0 in the Ukraine, although they remain at the top of Group B.
Wales and the Republic of Ireland both produced what could have been coach saving performances as the Welsh defeated Cyprus 5-2 and Steve Staunton's men drew 1-1 with Euro 2004 semifinalists Czech Republic.
But it was England's defeat that will cause the most headlines, as Steve McClaren's new formation of 3-5-2 backfired as the produced yet another dire performance.
Croatian fans have plenty to shout
Goals from Edouardo Silva and a goalkeeping howler from Paul Robinson, an effort sure to be on footballing bloopers tapes for years to come, sealed the visitor's fate as they return home to face a grim post mortem.
However, McClaren remained defiant in the face of his growing legion of detractors.
"It was my decision to change. We've lost the game so obviously the tactics did not work," he said.
"The team tried and the players did the jobs they were told to do. It has not worked and we have lost the game."
He also fully expected to be blast from the English press.
"It is part of the job," McClaren said.
"I have been around the scene for five years and I know what it entails. I pick the team, pick the tactics, the shape to win a game. If we win I accept the plaudits. If we lose I accept the criticism. That is part of the job."
Victorious coach Slaven Bilic was happy to deflect all praise onto his players.
"As my colleague Frank Rijkaard says, coaches might prepare the team but it is the players who win the game and all 14 players worked as one to get this victory," said the former defender who was famously part of the Croatian side who played in the 1998 World Cup semi-final.
Another former player now patrolling the sidelines, Italy coach Roberto Donadoni, was also full of praise for his players as they continued to recover from their poor start to qualifying.
"To come here and get a result may seem easy, but easy it certainly wasn't. In fact there were times when we really suffered," said Donadoni.
"We did well to stay patient and win the match, even if the sending-off did give us an advantage.
"I have to congratulate all of my players. They were good enough. As always there are things that we can improve on, but the spirit was right. Now we look forward with confidence.
Germany maintained their 100 percent record drawing to within a point of Group D leaders Czech Republic with a game in hand.
Germany make it 3 from 3
Polish-born striker Lukas Podolski scored a double to take his international goal tally to 23 in 38 internationals.
"We have continued where we left off at the World Cup," the 21 year old said.
"Slovakia are a tough team to play on their own turf but we started so well and took the game to them. We were clinical in front of goal and I was glad to grab a couple of goals."
The next round of qualifiers is on Nov. 15, although the majority of teams are not back in competitive action until March 24 next year.