It was the second time in that sequence of Isthmian south east defeats that Chi conceded late on.
Without right back Ryan Davidson, midfielder Emmett Dunn, and suspended top scorer Callum Overton, Miles Rutherford & Co were forced into changes.
Skipper Jamie Horncastle dropped back to cover for Davidson, Lewis Hyde partnered Ben Pashley in the centre of the defence, and Tyrone Madhani, available after a three-match suspension, replaced Dunn in the middle of the park.
A pitch inspection earlier on deemed the surface playable, but Storm Eunice had clearly left its mark at the Reachfields Stadium and in driving rain and swirling wind both teams had to deal with testing conditions from the outset.
The hosts won a free-kick early-doors which Tyler Sterling, on loan from Folkestone Invicta, whipped in and Chi players smuggled away for a corner.
At the other Ethan Prichard delivered a cross too close to Cannons keeper Henry Newcombe.
A speculative effort from Sterling, with three goals in the past two games, was easy enough for Chi custodian Kieran Magee before Luca Woodhouse grabbed the opener in the sixth minute as Magee’s defenders tried to walk the ball out of the box.
Ben Mendoza then fouled Jacob Gilbert. Sterling took the set-piece only to pick out an offside Riley Alford.
With the pitch cutting up the visitors literally struggled to get a foothold in the match.
Sterling had a shot blocked by opponents; James Rogers was well-in on Chichester midfielder Lloyd Rowlatt; Kaleem Haitham diverted Liam Smith’s delivery; before 17 minutes in Smith gave Magee something to think about with another cross.
Magee, who’d just taken a free-kick, came out swiftly to clear to Josh Clack. Clack had his shirt pulled and as a consequence his pass to Prichard didn’t come off.
Mendoza committed another foul, on Rogers this time, and Sterling sent his set-piece in, which Rob Hutchings hooked away, the ball getting caught by high winds and sailing out of the ground.
Sterling fizzed one narrowly over the frame of the goal at the mid-point and sixty seconds later Chi were level with Clack scoring his first goal in his second spell at the Oaklands Park outfit after a measured pass from Haitham got his teammate one-on-one with Newcombe.
A super Gilbert hit pulled a fine one-handed stop out of Magee and then Rowlatt and Horncastle combined but the final ball was just behind Clack.
Nice feet on a tricky surface by Haitham presented Clack with an opportunity which was bravely blocked, as was Prichard’s attempt too.
In a spell of Chi pressure, Madhani had a shot cleared and Clack strayed offside following a neat interchange.
Alford and Gilbert probed with Magee out to tidy up; Pashley steered the ball away for a corner that Hutchings headed firmly clear; and Prichard almost rounded Newcombe but for a heavy touch.
Sterling’s control then similarly let him down when he got in five minutes ahead of the break.
Next, Haitham’s cross caused Newcombe no trouble; Gilbert received the first yellow card of the match; and Sterling struck a set-piece over the top with the last kick of the half.
The wind dropped somewhat, but misplaced passes and other errors featured regularly, and unsurprisingly, in the second 45 as things got heavier and heavier.
Woodhouse overhit a ball to Alford in the first attack before Prichard drove just past the left hand post.
Pashley dealt calmly with a move involving Sterling, Woodhouse and Tom Walmsley.
Haitham then fired one inches wide; Prichard was bundled over after an opponent slipped on the ice rink surface; and the wind held up a cross of Sterling’s which Chi eventually cleared.
Woodhouse conceded a set-piece that came to nothing moments before the hosts lost Alford, and sub Jordan Sarfo was in the thick of it instantly with an attempt that wasn’t far off.
Newcombe denied Clack in the 57th minute and Pashley got a boot on the subsequent corner.
Another two came and went for Chi and then on the hour Gilbert blew a chance to shoot following a smart passage of play with Woodhouse and Sterling.
Connor Cheek cleared after Rowlatt and Haitham pressed before the Hythe No6 fouled Madhani only for a bit of Six Nations stuff from Hutchings as his free-kick sailed over the woodwork.
Rowlatt and Haitham set Prichard up for a decent opportunity which was wide of the mark, and Mendoza had an attempt blocked.
Clack and Hyde, both at the back stick, spurned two others when the subsequent corner came through everybody.
Hutchings caught Gilbert and the midfielder, with a bloody nose, was replaced by Mayhew on 78 minutes.
Chi turned a Sterling free-kick away before Sarfo broke down the left only for Prichard to clear once more.
Hutchings joined Rogers in Jake Woodman’s notepad before Sterling went close with a low drive.
Chi then had the ball in the back of the net after nice play by Mendoza, Pashley and Madhani but the referee’s assistant flagged for offside.
Mendoza picked up a booking for a challenge on Woodhouse.
Prichard got the set-piece away and the visitors countered down the right with Clack cracking an effort into the side-netting.
In the reverse fixture at Oaklands Park back in October, Chi looked to be heading for all three points after a first half wonder-goal from Prichard, until Gilbert popped up in the 88th minute with one of his own.
And here, Hythe nicked all three at exactly the same time in the game after Woodhouse broke swiftly, fed sub Mayhew, who rifled the winning goal in off the post.
Chi, pointless in their last three for the first time this season, remain in ninth place and welcome league leaders Hastings United to Oaklands Park next on Saturday 26th February (Kick Off 3pm).
Chichester – Magee, Horncastle, Hutchings, Madhani, Hyde, Pashley, Rowlatt, Prichard, Clack, Mendoza, Haitham. Subs: (Carroll, Oakwell-Boulton, Coote)