Eagles - booed by Rovers fans as he used to play for their bitter rivals Burnley - set up Kevin Davies to open the scoring after 93 seconds.
Blackburn goalkeeper Paul Robinson denied Eagles from long range on a number of occasions but on 61 the former England man turned his free-kick onto the post and Lee Chung-Yong was on hand to make it 2-0.
Jordan Rhodes pulled one back but too late for Rovers and Freedman admitted he enjoyed watching Eagles, who is known to be one of the more self-confident players in the squad.
"He's been performing very well - let's not tell him that, knowing Chris," joked Freedman.
"He's a good guy, he's a fine football player who's still getting better. It's up to me and my staff to try and put on sessions that test them every day and he is one that's certainly responding to training every day.
"Of course he can get better, there's a lot more to come. He has huge potential. His apprenticeship was at Man United, he's played in the Premier League. There's a lot more to come from Chris Eagles and I don't mind telling him that."
Bolton are unbeaten in six games since Freedman arrived from Crystal Palace and he said this was the best display so far.
"That's been the best performance in terms of all-round performance.
"I think we've actually played decent at Blackpool but I think as an all-round performance - defending very well at the end and our passing and moving, we played quite expansively with two wingers and I felt that we created opportunities.
"But I've been seeing it at the training ground. The lads have been working terrifically well, they've really responded to the methods."