Another closely fought game went the way of the opposition as high-flying Sporting Khalsa took all three points at Butlin Road.
Having edged the first period, Town went on to suffer their sixth home league defeat of the campaign thanks to a second-half double from Andre Landell.
Rugby boss Ian King made two changes to his starting line-up from the match four days previously against Loughborough, with Northampton Town work experience loanee Will Ronald in for Ayo Lekuti, and Silvano Obeng replacing Keiron Berry, as King tweaked his formation to operate with wing-backs for the first time in his tenure.
Simeon Cobourne bundled a threatening low ball across the face of the Valley goal early on, but it was the hosts that made the brighter start overall.
Harrison Nee's long ball out from defence was flicked on by the head of Obeng to see Jahvan Davidson-Miller show good speed to run on and fire in a low shot that Sporting keeper Brandon Ganley applied a strong one-handed save to keep it out.
Trey Charles had a shot blocked after Obeng's dinked cross had been laid back to him by Nee, and then Nee set Charles up again from a well-worked corner routine, but this time Charles made a mess of his shot from a good position.
Chay Tilt did volley one way off-target for the visitors, but it was generally Town that were on top, with Charles then dragging his effort wide from the edge of the box after he had shown neat control to a high ball into him.
Khalsa did start to exert some pressure on the Rugby defence in the approach to the break though, with Robbie Bunn drawing a double save from Paul Hathaway with back-to-back efforts from tight angles, and Callum Dolman shooting wide from distance.
Obeng's dangerous cross into the box was cleared away, before Hathaway saved a rising effort from Kristian Green, with the final chance of the half falling to the home side when debutant Ronald slid onto Nee's delivery to the back post - only to see Ganley down well to smother his attempt.
However, not for the first time in recent fixtures, Rugby were then pinned back from the start of a new half.
Landell's poked effort to Tilt's cross from the right had already seen Hathaway called into action before the Khalsa striker did the trick on 48 minutes with a fine header to James McGrady's cross from the other wing.
Landell then helped over an on-target header from Matt Fulloway, before scoring his second of the game with an instinctive connection to Tilt's low ball into the box which went through the body of Hathaway on the way into the net.
Town were back in it on 69 minutes though, after Obeng was clipped in the penalty area by Todd Ferrier as he was shaping to shoot, and Charles was his normal reliable self from the spot to stroke the ball into the bottom right hand corner.
The visitors responded well to Rugby's goal though, and Hathaway was soon pulling off a good save to Cobourne's effort to Landell's cross, and then Landell himself saw his shot deflected over for a corner.
McGrady and Tilt also both had shots blocked in close succession, with McGrady almost adding his side's third when he met Cobourne's searching cross but Hathaway's excellent point-blank stop denied him.
Charles then put one way-off target after sub Madundo Semahimbo had laid the ball back to him as Town pushed for a late equaliser.
Three successive deliveries into the box from Charles culminated in a goalmouth scramble which saw Davidson-Miller's back heel towards goal stopped on the line, with Tyreace Brown just unable to capitalise on the loose ball.
With the game deep into stoppage time, Rugby were reduced to ten men, after Charles incurred the wrath of referee Karl Donaghey and somehow was shown two simultaneous yellow cards for dissent after the award of a Khalsa free-kick in the middle of the pitch.
Valley Line-up: Hathaway; Summerfield, Brown, Thomas; Ronald, Nee, Edwards, Elliott; Charles, Obeng (Semahimbo 81'), Davidson-Miller. Subs not used: Francis, Lekuti, Sahota, Berry. Booked: Charles. Sent off: Charles.
