Daly slotted home from 14 yards following a clever pass from David Goodwillie, who had levelled just before the interval.
Flavio Paixao had claimed a richly-deserved opener for Hamilton and the bottom club were denied a strong penalty claim in the latter stages of the second half.
But Daly proved the difference after making his comeback in the final 20 minutes to move United two points behind fourth-placed Kilmarnock in the Clydesdale Bank Premier League.
"Jonny was feeling really good and doing all the running and working with the physio," Houston said. "The physio and our doctor wouldn't give him permission until we spoke to the guy who performed the operation.
"He told Jon `if you're feeling all right, get on with it'. Big Daly hasn't trained an awful lot for a few weeks but he was good for 20 minutes. I feel his presence helped. He had been doing well and scoring goals before he went out. Goodwillie sets him up brilliantly but it's a good finish from him."
Source: PA
Source: PA