The goalkeeper diverted the ball into his own net just after the hour mark to settle a scrappy encounter.
Town's number one keeper Scott Loach was absent with a sprained thumb, giving Henderson the chance to deputise in his absence, while midfielder Lee Martin was missing with a hamstring injury.
The two sides cancelled themselves out in the opening stages although Blackburn goalkeeper Jake Kean did comfortably save a speculative Guirane N'Daw effort from 30 yards after 20 minutes.
Aaron Mclean should have done better with a close-range header following an Aaron Cresswell corner, but the striker failed to trouble Kean, while at the other end, Danny Murphy's shot was similarly wide of the mark.
There had been no shortage of effort but the lack of cutting edge had been more than evident in a lacklustre first 45 minutes as neither side had showed the quality required for a concerted push for the npower Championship play-offs.
A free-kick from Morten Gamst Pedersen floated into Henderson's hands as neither side could find the killer touch in front of goal. It was Pedersen's final participation in the action as he was replaced by former Town striker DJ Campbell after 57 minutes.
And Rovers were ahead within four minutes of the striker's arrival. A corner by Murphy to the far post was met by Grant Hanley whose effort was blocked by Luke Chambers before Henderson got the final touch en route to the net.
It was a messy goal in a messy game but it did mean the Tractor Boys were compelled to go on the attack. Mclean tried his luck from 30 yards as McCarthy tried to salvage something.
But Ipswich were unable to force a leveller and are now just one point above the drop zone.