Clinical strikes from Michael Higdon after 41 and 65 minutes saw Saints claim their first points away from home this term to deny United a third straight success.
Prince Buaben powered in an 86th-minute free-kick to set up a tense finale but United suffered a third home loss of the campaign.
"No complaints - the better team won," said Houston. "I thought St Mirren were hungrier than us, passed the ball better than us and all the things that we're good at we didn't do. The opposition were hungrier and had more desire to win the match."
Source: PA
Source: PA