Walcott justified Fabio Capello's decision to keep faith in him - and jettison David Beckham - as Croatia suffered a first ever defeat in a competitive game at home.
An equally impressive Rooney added a fourth for good measure as Slaven Bilic's side finished in a demoralised state after the 53rd minute sending off of Robert Kovac.
All Croatia could manage in reply in this Group Six clash was a late consolation effort from substitute Mario Mandzukic.
It was all so different to two years ago in the same stadium, when then England coach Steve McClaren opted for an ill-fated 3-5-2 formation and saw his side lose 2-0 in a Euro 2008 qualifier.
But England appear a different animal under Capello and, although this was only the second step on the long road to the 2010 finals in South Africa, the signs are encouraging after one of their most convincing displays in living memory.
Capello showed positive intent with the line-up he sent out in the Maksimir Stadium and his players backed him up with a performance of grit and commitment harnessed to their attacking abilities.
Walcott will attract all the headlines and rightly so more than two years after being the shock inclusion in Sven-Goran Eriksson's 2006 World Cup squad.
He only made his full debut for his country in Saturday's 2-0 win over Andorra in Barcelona but did enough to again keep Beckham on the bench until the closing stages.
But he showed great composure in netting England's first competitive hat-trick since Michael Owen's treble against Germany in Munich seven years ago in another World Cup qualifier.
Now a question mark will inevitably hang over whether the 33-year-old Beckham will start another game for his country after this Walcott show.
Capello opted not to man-mark midfield play-maker Luka Modric and the Tottenham player saw plenty of the ball during the early stages as the focal point of his side's attacks.
David James needed two attempts to grasp a shot drilled straight at him by Danijel Pranjic and then failed to hold on to a deep corner from Darijo Srna and would have been relieved to see Vedran Corluka drill the loose ball into the side-netting.
The pressure steadily mounted on England although resolute defending denied the home side any clear-cut opportunities.
The visitors went ahead through Walcott in the 26th minute - but they were given a helping hand by the Croatian defence.
Pranjic's clearance rebounding off Josip Simunic into the path of Walcott but the teenager made the most of his fortune as he drilled a fierce low shot across Stipe Pletikosa into the corner of the net.
Walcott could have added a second from a similar position soon afterwards but this time Pletikosa was able to tip his effort around the post.
Mladen Petric had a fierce low drive blocked but the Croatians failed to cause any major problems in the opening 45 minutes.
And they became increasingly wary of the pace of Walcott who was cynically sent crashing to the ground off the ball by Simunic after one lightning run - a challenge which earned him a 38th minute yellow card.
England looked composed and Pletikosa did well to get his body behind a low, skimming free-kick from Frank Lampard.
Then after 53 minutes Croatia were reduced to 10 men when Kovac was sent off for an aerial challenge which left Joe Cole bloodied - and replaced by Jermaine Jenas.
England almost instantly made their numerical advantage count - with Walcott striking for the second time.
Heskey and Rooney were involved in the build-up before the overlapping Walcott had time to pick his spot and send a low shot across Pletikosa, mirroring his effort for the first goal.
England were now rampant and in the 63rd minute Rooney ended his 11 month international scoring drought - all that he deserved after a marvellous display.
Ashley Cole won the ball off Srna, picked out the run of Jenas and his low cross from the left flank was clinically despatched by the Manchester United star.
Lampard had an effort ruled out for offside before Mandzukic beat James from close range with 12 minutes remaining.
But Walcott ended any hopes of a late Croatian revival as he collected a Rooney pass and clipped the ball wide of Pletikosa for his hat-trick.