The 66-year-old was delighted with his team's performance and reserved special praise for his squad's reaction following Franck Ribery's sending off in the first half
The game got off to a bad start for the hosts after Franck Ribery was sent off in the 33rd minute following a squabble with Henrique Sereno, but they responded through strikes by Mario Gomez, David Alaba and Toni Kroos after the break.
The coach also stated that he is confident of a great second part of the season once Bastian Schweinsteiger and Arjen Robben return to full fitness.
"We fully deserved to win, and it was the right margin of victory too. We dominated the match and translated our footballing class into goals," Heynckes told Bayern Munich's official website.
"Koln parked the bus today. I’ve rarely seen a team with such a defensive approach.
"Ribery’s sending off made it even more difficult, but my team responded magnificently. We struck at the decisive moments, we let them have nothing at all, and we kept our discipline.
"Once we have Schweinsteiger [Bastian] back, and once Robben [Arjen] is fully fit again, we’ll certainly do well in the second half of the season.”
Following the win over Koln, Bayern Munich ensured their place at the top of the Bundesliga over the winter break.