Goalkeeper Simon Sluga’s throw was stolen off Ryan Tunnicliffe’s toe by Jacob Murphy on the edge of Town’s area and the wide man picked out Stephen Fletcher at the back post to where the Scottish international nodded down for the tap-in.
It was a blow that the Hatters could not recover from after a promising first half performance.
Graeme Jones made three changes to the side that lost to West Bromwich Albion, with Kazenga LuaLua handed his first start of the season along with Andrew Shinnie and James Bree.
That was at the expense of Pelly-Ruddock Mpanzu - the first league game the midfielder had not started since the 2-1 home win over Mansfield on April 2, 2018 - Dan Potts and Callum McManaman.
It started so well for Town though, and Tunnicliffe will be kicking himself to have blazed over from 12 yards in the ninth minute after receiving the ball back from LuaLua.
The winger then stung keeper Keiren Westwood’s palms from distance and, though it proved too hot to handle, the rebound didn’t fall to a Town player.
Hatters keeper Sluga produced a wonderful flying save to beat away Harris’ curler, moments after Harry Cornick beat the last defender to a long ball but somehow had the ball nicked away from him.
Shinnie almost left egg on Westwood’s face, volleying back the keeper’s poor clearance after James Collins had chased him down, but the number one recovered to tip over.
Sonny Bradley saw a header from Jacob Butterfield’s corner, dip just over and when the teams walked off at the break, small sections of the home support turned on their side.
However, the hosts improved after half time and took the lead ten minutes in through Harris.
Martin Cranie then had to depart, pulling up after clearance and getting stretchered off, for Bolton to replace him.
Fletcher had the ball in Luton’s net in the 66th minute but it was ruled offside and the Scottish international then saw a header fly dangerously close with Sluga well beaten.
Luton laboured at the other end until late on but when they found themselves deep in Wednesday territory Cornick swung and missed, while Bolton, making his league debut for Luton, had a heavy touch in the penalty area which allowed a recovering block and, with that, a chance to take a point from the contest.
TOWN: Sluga, Cranie (Bolton 59), Pearson, Bradley (c), Bree, Butterfield (Mpanzu 74), Shinnie, Tunnicliffe, LuaLua (Brown 69), Collins, Cornick. Subs not used: Lee, Moncur, Jones, Shea.
REFEREE: David Webb
ATT: 23,353
