The powerful frontman latched on to a great flick from Gabby Agbonlahor to score the only goal of the game on 21 minutes and give Villa a club record sixth consecutive away win.
It was a great finish from former Bluenose Heskey as he rifled the ball in on the half volley giving England teammate David James no chance.
Prior to the game, Martin O'Neill had changed the 4-5-1 formation that has served Villa so well this season in order to accommodate his £3.5m buy from Wigan.
And the more traditional 4-4-2 system worked superbly in the first half with James Milner and rare starter Craig Gardner posing Pompey problems on the wings.
The Claret and Blue defended in stout fashion to block any early advances from the home side and managed to take the lead slightly against the run of play.
Sylvain Distin, usually so commanding in the air, was beaten by Agbonlahor and Heskey made no mistake when faced with the imposing figure of James.
Villa then had a chance to increase their lead as Agbonlahor found himself through one on one but the speedy striker somehow managed to steer his shot wide.
Dissent
Glen Johnson tried to reply for Portsmouth before the half time whistle but his tame shot failed to trouble Brad Friedel and Nadir Belhadj wasted a good chance.
Algerian born defender Belhadj played one other notable part in the first 45 minutes as he disgracefully hacked down Gardner. The Villa midfielder was advancing down the right before being scythed down from behind by the Portsmouth left back.
Belhadj was booked and received his just rewards in the second half as he was sent off for dissent.
After the break, Pompey stepped it up a notch and really peppered the Villa area with corner after corner.
But they couldn't make any of their opportunities count with Peter Crouch and late sub John Utaka both wasting good chances; the latter seeing his run halted by Friedel as Tony Adams looked on in dismay.
The former Arsenal defender turned Pompey boss has now won just two games of his 19 games in charge at Fratton Park and many fans will now be calling for his dismissal.
To be fair to Pompey, they played well enough and on another day they may have claimed all three points.
But Villa are simply irrepressible at the moment and they have really got into the groove of winning scrappy games.
Unity
It's a habit that could take them all the way to the top if they can keep it up and with new signing Heskey in this sort of form, the Claret and Blue are set to prosper.
Despite missing influential skipper Martin Laursen, wing wizard Ashley Young and midfield scrapper Nigel Reo-Coker, Villa registered another victory.
Zat Knight and his fellow stand-ins have really stood up to be counted and the big defender, in particular, can really be proud of a fantastic display against Pompey.
Knight was also excellent against Arsenal on Boxing Day and the former Fulham man is really staking his claim for a regular starting role.
Villa have a massive amount of strength and unity running through the squad at present and Heskey must be very impressed with his new teammates.
He has now proved that he can add to the obvious ability already inhabiting Villa Park and he will be hoping to continue his goalscoring start against former club Wigan on Saturday.
Villa will share Heskey's aim and another victory would see them reach an amazing 50 point tally from just 24 games.
Title challengers anyone?