The Aston Villa striker had not hit the target in an important match for his country since netting against Denmark in Japan seven years ago. However, Heskey was on hand to effectively kill off the contest in first-half stoppage-time with the simplest of tap-ins, after his former Villa team-mate Gareth Barry had settled England's nerves with the opener minutes earlier.
For Barry, it was the perfect end to a week in which he had ended his 12-year stay at Villa Park and made the £12million switch to Manchester City. Then Wayne Rooney - with his eighth goal in his last six England appearances - and a Frank Lampard penalty gave a flattering look to the scoreline in the second period.
England were as disappointing in the opening half hour as they were in the first half of a UEFA EURO 2008 qualifier against Andorra in Barcelona, during Steve McClaren's reign. However, under Fabio Capello they have acquired the habit of being able to eke out results when not firing on all cylinders, as well as producing majestic performances such as the one when they beat Croatia 4-1 nine months ago.
Victory maintained their perfect record in Group 6, and they will have one foot in the finals in South Africa next summer if they dispose of bottom-placed Andorra at Wembley on Wednesday. However, Capello will not be fooled by the margin of victory, and there are sure to be plenty of harsh words when he sits down with his players to watch a re-run of this game next week back at the team's Hertfordshire base.
Capello made four changes - three of them enforced - to the side which had been below their best in overcoming Ukraine 2-1 at Wembley in April. West Ham goalkeeper Robert Green was handed his first England start in place of the injured David James, with Matthew Upson and Theo Walcott back in the side for the sidelined Rio Ferdinand and Aaron Lennon.
Fit-again Heskey was preferred up front to Peter Crouch despite the Portsmouth player grabbing his 15th goal in 33 internationals against Ukraine. Kazakhstan have a reputation for playing well in the first half of their qualifiers and they knocked an inept England out of their stride in the early stages.
In the first minute Glen Johnson was guilty of giving the ball away and allowed Alexandr Kirov to send in a low centre and it needed captain John Terry to make a last-ditch interception to deny Sergey Ostapenko. Capello was more animated than usual at his team's poor start, pacing menacingly around the dug-out, and at one juncture appeared to be involved in a heated verbal exchange with Ashley Cole.
Barry's 16th-minute booking for a challenge on Zhambyl Kukeyez means he is suspended for the Andorra match. A minute later, the stadium erupted when Ostapenko headed in an inswinging free-kick from Kukeyez, but the joy was cut short as he had strayed marginally offside.
It was to be Ostapenko's last meaningful contribution before he was carried off on a stretcher and replaced by Sabyrkhan Ibrayev. England slowly began to get a foothold in the game and a low shot from Heskey was turned onto the post by goalkeeper Alexandr Mokin after good play by Wayne Rooney.
A John Terry header from a Frank Lampard corner was then saved by Mokin before England took control with two goals in six minutes before the interval. Barry broke the deadlock after 40 minutes with his first competitive goal for his country. Steven Gerrard sent over a deep cross after playing a short corner with Ashley Cole, and Barry had the time and space to pick his spot and head past Mokin.
Then on the stroke of half-time came that Heskey rarity. Gerrard was again involved in the build-up with his deflected cross taking Mokin by surprise, and Heskey was on hand to tuck away the loose ball.
Capello took off the ineffective Walcott at half-time and brought on Shaun Wright-Phillips, who also failed to make much of an impression. There was little that was memorable about the second 45 minutes before a piece of quick thinking by Rooney brought him the third goal with 18 minutes remaining.
Johnson's centre was turned goalwards by the Manchester United striker, only for Mokin to keep out his effort at full length. But Rooney was alert to the rebound and his scissor kick ended up in the roof of the net. Lampard then took England's goal tally in the group stages to 20 when he drilled home a penalty after Heskey had been brought down by Renat Abdulin.