Holden initially suffered a serious knee injury in Wanderers' Premier League game at Manchester United in March 2011.
A challenge from United defender Johnny Evans left the 27-year-old requiring 26 stitches in a wound to his left knee.
Wanderers were seventh in the top flight at the time and, although Holden made a comeback against Aston Villa in the League Cup last season, a subsequent cartilage problem prevented him from playing a single league game as his team-mates were relegated to the Championship.
Trotters fans were finally granted an opportunity to see him in action during a 3-0 reserve victory over Oldham at Leyland, much to the delight of Freedman.
"It was great to see him out there," the former Crystal Palace boss told The Bolton News. "To get 65 minutes, we are very pleased, and a very good 65 minutes at that. I thought he was very influential in the game as well.
"Having been out for so long but to be involved in most of the match is very encouraging and also very pleasing for Stuart."
Freedman has hinted Holden and young forward Josh Vela, himself returning from a knee injury suffered in pre-season, could feature in the FA Cup third-round replay at Sunderland in six days' time but was quick to urge patience.
"We have got to remember that because he's been out for so long, we have to put Stuart first and foremost," Freedman added.
"He has got to be given time, and he has been given that. He has to be given a pat on the back as well."