Albion striker Scott Ramsay kicked off his Bognor loan spell with the calmly taken penalty which ruined Barry Lloyd's homecoming.
Ramsay grabbed the ball from stand-in skipper Jamie Howell and slotted the 68th minute goal which proved the turning point in this hard fought Ryman League derby.
It was Rocks' second spot kick of the afternoon, following Howell's first half failure. They secured victory with a Nicky Wyatt strike six minutes into added time.
Victory took Bognor level on points with leaders Aylesbury but boss Jack Pearce admitted his men had ridden their luck.
He said: "We've got a very good result with six or seven of our players performing below par. We defended well but the score flattered us."
Lloyd, who never enjoyed a home win over the old rivals in his first stint as Worthing manager, agreed his side had been unlucky.
He said: "There wasn't a lot between the two teams. They are top and they get the breaks. We've got to up our game another 20 per cent and results will start coming."
Both bosses backed Lee Bonaldi on the penalties.
The first, on 39 minutes, was the main feature of a dull opening half as James Wastell saved Howell's tame effort following Darren Baxter's lunge on Richard Hudson.
Wastell also blocked a Ramsay drive and Kevin Murphy headed over as Rocks shaded the first half.
Worthing have adopted a more thoughtful style of play under Lloyd and it almost brought them a 49th minute breakthrough.
Ben Carrington slid a pass out to Gavin Geddes, who did well in the unusual position of right midfield. Geddes's cross was pinpoint accurate but Gavin Jones headed against the inside of the post and then saw his follow-up blocked by Craig Stoner.
The busy Jones was also denied by a superb covering tackle from Jodey Rowland.
Other than that, the hosts' attacking work generally bounced off a defence marshalled by David Wright.
It was still a surprise when Rocks went ahead, thanks to Andrew Beech's challenge on Matt Russell on the edge of the area as they contested Miles Rutherford's pass.
Lloyd went route one for the final minutes, sending Damian Webber on up front.
But it was the Bognor substitutes who had the final say as Worthing old boy Simon Funnell nicked the ball away from Andy Alexander and released Wyatt to score.
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