Wanderers went ahead through a Rob Hall goal before Jermaine Easter levelled for the Lions.
But Jermaine Beckford's goal two minutes before half-time and Andre Moritz's first goal in a Trotters shirt saw them extend their unbeaten run to six games.
Freedman acknowledged the importance of Saturday's victory and said: "It's not a relief but I felt that a win was crucial today.
"It's important to get that first home win but I think that the majority of performances at home have been good recently.
"We've put behind us some bad form at the start of the season which we didn't shy away from because we knew there were areas where we could improve.
"I feel if we can keep our feet on the ground we will start to really pick up points and move up the division.
"I feel that the timing of the goals today was really good for us but I felt that we were a threat throughout the match.
"Even though they were coming at us in the last 20 minutes, I still think that we looked in control and were comfortable and good value for the win.
"The third goal was a quality goal and I think that 3-1 was a deserved result and it sealed off an all-round great display."
Millwall manager Steve Lomas was really unhappy with Bolton's first goal and believed his side could have had a penalty.
Nicky Bailey was taken off the pitch after a head injury but referee Graham Scott chose to continue the game.
Lomas said: "We were bitterly disappointed about the first goal. It was a clear head knock.
"It's the first head knock of the season that I've seen that the game has then played on and Nicky's a very important player for us in that situation because he plays in the centre of midfield.
"The referee said his microphone wasn't working because the fourth official was telling him in his microphone that it was a head knock.
"We seem to be getting the short end of the stick with decisions lately and we could have had a couple of penalty shouts there as well."
The Lions have now gone five games without a win and are just three points clear of the relegation zone and Lomas wants to see more defensive resolve from his side.
He added: "We showed resilience to get back in the game but we shot ourselves in the foot conceding that goal just before half-time.
"We're not far away but we need to tighten up at the back or you're not going to pick up results in games like this."