Ryan Bertrand, Alli, Sturridge, Jesse Lingard and Theo Walcott replaced Danny Rose, Eric Dier, Harry Kane, Adam Lallana and Raheem Sterling, the last three being unavailable for the game through injury.
Bertrand, though, lasted only 19 minutes before being hit by a hamstring injury and had to be replaced by Rose and England have called up Arsenal’s Kieran Gibbs as a replacement.
But a constant in the England team – skipper Rooney – set the tone from the start at Wembley, where the crowd was an incredible 81,781.
The Manchester United captain, despite playing in a deep-lying midfield role, produced England’s first two efforts.
After a free-kick was charged down, Rooney unleashed a shot which was well saved by the diving Andrew Hogg, Malta’s English-born goalkeeper.
Lingard, on his debut, then shot over when he should have done better and Hogg saved well again from a Alli header.