High-flying Loughborough Dynamo secured the points at the death at Butlin Road, when Town's Roger Lee diverted past his own keeper in the sixth minute of added-time.
It was a cruel conclusion for Valley, who had taken the lead when Dan Summerfield smashed home Caine Elliott's lay-back on 29 minutes.
Town started with the same eleven that had kicked-off the previous week's narrow home defeat to another team at the top of the table Anstey, and it was the hosts that had the game's first real chance when Silvano Obeng fired his effort straight at Dynamo keeper Lewis King after he had shown good strength and purpose to turn his marker in the box and surge goalwards.
King's counterpart Nykah Liburd-Hines then gathered a low shot from Loughborough's George Ball, before Rugby were back on the attack again - with a potentially dangerous Summerfield cross neatly taken by King.
A threatening Ball delivery from the by-line was just cleared away, and from the resulting corner David Chapman fired one into the side-netting.
Robert Norris's well-executed volley bounced just wide as the visitors probed for the opener, but Rugby continued to cause problems themselves, with a Courtney Lashley cross requiring a sliding block and then Caine Elliott and Lashley combining well to set up Jordan Wilson for a shot from the edge of the penalty area that cannoned back off the crossbar.
The chances continued to flow at both ends of the pitch, with Liburd-Hines pushing away Evan Garnett's low effort to the near post and Rugby's Josh Thomas guiding one over the bar from distance after he had stolen possession in the middle of the pitch.
Town's breakthrough came after Lashley's deep cross was met by Elliott, who in turn laid the ball back into the path of Summerfield to steer it past King and into the net.
A series of chances followed for the visitors, with Liburd-Hines gathering efforts from Ball, Connor Furey, Garnett and Rio Molyneaux in relatively close succession.
The hosts finished the half with a decent spell though, and another promising Lashley cross was cleared by Gianluca Bucci and then Thomas headed Karabo Motshweni's corner to the near post off-target.
Loughborough started the new period with added purpose, with Ball soon curling one wide.
Town did have a great opportunity to double their lead though, when Obeng ran onto a long ball forward by Summerfield and then squared it to Karabo Motshweni - whose effort was kept out by a good stop by King.
The visitors upped the pressure on Rugby after that missed chance, with Robert Norris putting one over the bar, and Tom Marshall and Jonathan White both having shots blocked in close succession.
Marshall's strong run into the box ended with a near-post effort that was pushed away by Liburd-Hines at his near post to launch a series of corners - which saw Mitchell Robinson and Norris both have attempts deflected off-target. White and Marshall then struck the crossbar within seconds of each other as Dynamo went even closer to an equaliser.
For Rugby, Motshweni and Thomas did have free-kicks from potentially dangerous positions near the Loughborough box, but Motshweni's rising strike was taken high by King and Thomas's drifted over.
Another good chance for the hosts went begging after sub David Kolodynski helped Summerfield's pass onto Obeng, but after initially being thwarted by King, the lofty striker then lifted the ball high and wide of the frame. Loughborough finally broke Town's brave resistance on 83 minutes though, when Mo Bangura's low cross was met by a composed finish from Garnett.
Molyneaux chipped one onto the roof of the Rugby net and Garnett's shot on the turn was taken by Liburd-Hines, as the visitors sensed that a victory could be theirs, although the home side did then have the ball in the net when Ryan Sahota showed a neat control and finish to another Kolodynski attempted assist - only to see the goal ruled out by a debatable offside flag.
The late hammer-blow for Valley came after Bangura's jinking run created space for himself on the left, and his delivery across the crowded penalty area bounced off Lee's leg and into the net.
Line-up: Liburd-Hines; Summerfield, Thomas Mace, Francis; Elliott, Fitzharris (Lee), Motshweni; Wilson (Kolodynski), Lashley (Sahota), Obeng. Subs not used: Recci, Kirby-Moore. Bookings: Francis, Fitzharris, Sahota.