After a trio of 2-2 stalemates on the road, Pompey finally made it across the winning line despite being reduced to 10 men and conceding a late consolation goal.
Whittingham said: "It's a pleasing result because we've done a lot of hard work during the week on protecting leads when we have them. I think we did that very well today.
"Out of all the games we've played so far, we've probably created the least amount of chances for us. But that's the balance we're looking for - where you create chances, you score goals but also make sure you're hard to beat.
"It's a great result and all the players need a big pat on the back because all the ideas we've had have come to fruition."
The hosts suffered a second successive home defeat as Ricky Holmes and Simon Ferry made the most of some indifferent defending.
The victory was marred only by an 84th-minute red card for full-back Yassin Moutaouakil for taking a kick at Burton winger Jimmy Phillips and a late strike for the hosts.
Whittingham said: "You can't kick out even if you feel there has been an injustice and Yassin left the referee with no choice but to send him off."
The visitors looked the more creative side and took the lead in the 33rd minute. Jordan Pickford did well to keep out a Patrick Agyemang header, but Holmes reacted quickly to hook home the loose ball from a tight angle.
Only a stunning one-handed save by Pickford kept Andy Barcham off the scoresheet as Burton suffered more defensive jitters.
Ferry increased the advantage six minutes after the break when he stabbed in a close-range shot after a Holmes effort had been partially saved by Pickford.
Defender Zander Diamond netted a consolation goal for Burton in the fifth minute of added time but it was too little too late.