Lonergan hauled down David McGoldrick in the area in the 55th minute and Ipswich's top scorer shot home the penalty that made the difference in a tight affair.
Bolton's struggle this season looked like being eased after a promising first half which saw them enjoy the best of the chances at Portman Road, but they offered little following Ipswich's breakthrough.
Bolton manager Freedman said: "It was a very disappointing result. We felt in the first 45 minutes that we were by far the better side, creating two or three opportunities.
"There was not a lot in it, but a rush of blood in the second half was the difference.
"Andy Lonergan has been fantastic for us and we have no blame culture at this football club.
"The one disappointing thing is that we didn't create enough in the final 20 minutes.
"When these things happen, we have to make sure we stick together and not let our heads go down. These small moments are hurting us badly right now."
While Bolton were left to lick their wounds, Ipswich remain on the cusp of a top-six spot following a resolute, if unspectacular, performance.
Lonergan was forced to tip Aaron Cresswell's thunderbolt of a shot over the bar but Bolton had the best of the first-half chances through Mark Davies and Neil Danns - the latter seeing his effort smartly stopped by Dean Gerken when clean through.
McGoldrick's penalty, coming after he failed to score his previous two, changed the complexion of the match and Ipswich ultimately deserved the three points.
The winning margin could have been greater, with McGoldrick just missing the far post minutes after giving Ipswich the lead and the industrious Stephen Hunt testing Lonergan from distance.
Ipswich manager Mick McCarthy said: "There was never any doubt he (McGoldrick) would take the penalty.
"David McGoldrick epitomises us. He ran back 50 yards to tackle (Chris) Eagles when his job is to stick the ball in the net."
After watching his side toil to another three points, McCarthy was typically honest in his post-match assessment.
He said: "I didn't think, one to 11, we did enough in the first half but it is nice to sit in here when we have won like that.
"We are not great, we are not a silky football team. But we are a stubborn and hard-working bunch with a really good team spirit.
"We have got a good squad. It is not a big one, but it is a good one."