The Spaniard was delighted after overseeing his first win over the Ruhr outfit, though Arjen Robben admitted the match was more even than the scoreline suggests
The Bavarians were on the back foot for much of the initial period before Mario Gotze opened the floodgates against his former side at Signal Iduna Park in the second half.
And Guardiola believes die Roten's determined efforts to shut out Dortmund's danger men paid dividends before they could bring their own quality to bear later in the game.
"We are happy because we beat the best team at counterattacks in the world," the 42-year-old told reporters.
"We knew we had to control the first touches of [Robert] Lewandowski and [Henrikh] Mkhitaryan. If you let them run, they're unstoppable.
"Our first 15 minutes were good, the next 30 not so much. In the second half with Thiago [Alcantara], Gotze, [Philipp] Lahm and [Toni] Kroos, we played very well."
Goalkeeper Manuel Neuer likewise praised his team-mates' defensive attention, stating: "We always stayed calm and organised. We did not want Dortmund to catch us on the counter and we managed to do that well.
"The most important thing is that we won. And we won deservedly. We can go home relaxed now."
However, goal-scorer Arjen Robben believes the German champions' superiority was not as marked as the final score suggested.
"The 1-0 was very important, but we must not exaggerate," the Netherlands international said.
"It looks like a clear win, but for me it was an even match. At the end we had plenty of space and we took advantage of it very well."
The German champions have nevertheless opened up a seven-point gap between themselves and their fiercest title rivals at the top of the Bundesliga.