Ashley Barnes was brought on for Jay Rodriguez with 20 minutes remaining, drawing the ire of some fans on social media.
But it was Brighton duo Jakub Moder and Alexis MacAllister who had the biggest impact, both involved in goals with their first touch, Moder crossing for Neal Maupay to equalise on 73 minutes, before MacAllister netted what proved to be the winner five minutes later.
Burnley were left chasing the game, with Josh Brownhill coming on for Dwight McNeil, and Matej Vydra for Jack Cork, and Dyche said: “(It was) the feel of the game and what the game required at that time.
“Barnesy defends very well from the front and I thought in the second half we didn't do that as well as we did first half.
”That was my thinking, to get Barnesy on who can activate from that position on the defensive side but also to attack.
“His link with Woody has been well spoken about for a few seasons.”
Rodriguez got the nod to start with Chris Wood, ahead of Barnes and Vydra, while Cork edged out Brownhill, and Dyche admitted they were tough decisions: “Very difficult. They are all good players and all want to play but you can only pick 11.
”We want that competitive element quite obviously, and it is there, we saw it in pre-season and we want it to continue.
“We want players to be chomping at the bit to try and play.
”He (Vydra) is just behind the curve slightly so he will get more football over the next week or so and keep adding to his fitness.”