Wanderers fell behind 10 minutes after half-time to a header from Clarets defender David Edgar and Freedman elected to introduce strike duo Craig Davies and David Ngog.
The Reebok Stadium faithful voiced clear displease at seeing Marvin Sordell and on-loan Southampton winger Steve De Ridder leave the action, the latter having provided rare moments of invention in a disjointed performance up until that point.
But Davies converted Lee Chung-yong's left-wing cross, his first goal since joining from Barnsley last month, before former Liverpool man Ngog showed presence of mind to turn home Jay Spearing's speculative 81st-minute drive.
Nevertheless, Freedman resisted invitations to crow about his changes at the post-match press conference.
"Sometimes you get them right, sometimes you get them wrong - hopefully more right than wrong," he said.
"I understand the fans - everybody wants to win, everybody wants to see their favourite player. I completely understand that, I'm a football fan myself.
"But I'm a professional guy making professional decisions. Sometimes I take players off because they've got a card or for a tactical reason.
"Steve De Ridder hasn't played enough football so I had to take him off early. It's not something I would like to have done but I had to do it.
"I felt we made the subs to try and change the dynamic of the game. We felt that it was a tight game in midfield so went a bit longer, over the top and it worked for us. I'll never shy away from big decisions, I've done it as a player and I've done it as a coach."