A moment of controversy in first-half injury time proved crucial as Bognor slipped to their second home defeat in five days.
Rocks keeper Dan Lincoln was judged to have handled outside the box and was red-carded - and Dorking's Lewis Taylor thumped home the free-kick in the D.
It seemed Lincoln felt he was not outside the box and Rocks players and officials questioned whether he should have been booked rather than red-carded.
Bognor battled bravely in the second half but missed one-on-ones in both halves cost them dear and Dorking held out for a 1-0 win and the points.
It was tenth versus first at the Lane with ex-Bognor duo Jason Prior and Sami El-Abd both in the leaders' line-up as they returned to a club they both served well.
Bognor had two of their Pompey loanees back – striker Dan Smith and midfielder Freddie Read – but another, forward Brad Lethbridge, was ill.
With Read coming into the starting line-up, Tommy Block was on the bench ahead of a second trial with Scottish Premiership side Hibernian.
Gary Charman was fit to start in defence after sitting out the second half of Tuesday's loss to Enfield.
The Rocks were keen to get the defeat to Enfield out of their system at the start of a run of games against leading sides, with visits to Kingstonian and Worthing up next.
There was no noticeable reaction – favourable or otherwise – when El-Abd and Prior's names were read out in the line-up before kick-off.
Winger Mason Walsh was awarded player of the month for November.
It was a fairly even opening to the game with both sides stringing some nice passes together but not finding sight of goal in the first ten minutes.
There were half-hearted claims for a Rocks penalty on nine minutes as a Dorking defender appeared to handle as he fell with Smith trying to get past him.
Dorking's first shot at goal was a weak, wide one from James McShane after Reece Hall squared to him 15 yards out.
Walsh worked space for a decent cross from the left but keeper Slavomir Huk plucked it out of the rainy air. At the other end Prior's sidefooted effort following a cross from the right was deflected for a corner.
Walsh was Bognor's most dangerous operator and wasn't far off target from outside the box on 17 minutes.
Dorking wasted a free-kick a couple of feet outside the box as Charman cleared.
Taylor fizzed a low drive only just wide of Lincoln's right-hand post after Read gave the ball away in his own half.
On 26 minutes Muitt had what looked like it was going to be a cross from wide left but turned into a very good shot that Huk had to punch away from beneath his bar.
Taylor was booked just before the half-hour for a foul on Calvin Davies.
Smith missed a wonderful opportunity to put Bognor ahead on 30 minutes when he met Muitt's cross at the far post but mis-hit it wide from close in.
Dorking picked up a quick second booking when JJ O'Sullivan cynically hauled back Walsh – and from the free kick Joe Tomlinson went on a run that ended with his shot being put behind for a corner via a post. Harvey Whyte almost got on the end of it but El-Abd cleared.
A weak clearance from Huk led to Bognor pressure that saw Muitt put through for a shot across the keeper but it went wide of the far post.
Lincoln pulled off a top-class save on 42 minutes when Hall volleyed goalwards after El-Abd miscued a shot high into the air. Then Whyte went clear and drew a save out of Huk as he shot low across the keeper.
The game took a dramatic turn in first-half injury time when Lincoln was sent off for allegedly handling the ball very marginally outside the area. Lincoln protested his innocence, to no avail. Whether it should have been a red or yellow card was hotly debated
To add insult to injury, Taylor curled in the free-kick immediately after Ricardo Texeira came on for the unlucky Walsh to go in goal.
At the break Rocks skipper Whyte and manager Jack Pearce both attempted to speak to the officials – whether they were arguing over whether Lincoln was outside his box, or whether, if he was, he should have been sent off rather than booked, was not clear.
Sam Beard came on for the booked O'Sullivan after the break for Dorking.
Bognor's second half didn't start any better than their first half ended when Davies went down with what looked a serious ankle injury after clearing a cross. He was initially okay to carry on after treatment but ten minutes later Davies had to give into the injury and Block came on to take his place.
Bognor almost gifted Dorking a second goal with some comical defending on the hour. Texeira was struggling in goal but the Rocks were at least preventing Wanderers scoring a killer second.
A rare Rocks attack set up by Tomlinson's surging run ended with Read and Whyte playing in Muitt but there was no real power in his low shot and Huk got down to hold it.
Rob Sheridan was Dorking's second sub, replacing Hall on 72. Tomlinson, shortly before being named man of the match, cleared a shot off the line as Dorking looked all set for number two with 11 minutes to go.
Bognor threw caution to the wind on 82 minutes by bringing on striker Jimmy Wild for Charman.
Dorking missed a chance to wrap it in a goalmouth scramble, then Read had a shot blocked at the other end.
In four added-on minutes Muitt went through again with only the keeper to beat but again his shot, although well struck, was blocked by Huk.
They had one last chance to rescue a point when every outfield player went forward for a Muitt free-kick from wide on the right, and there were some appeals for a handball, but it wasn't given – and that was Bognor's last chance of salvation.
So it was a bad end to a tough week – and Bognor must now lift themselves for a trip to face Kingstonian next Saturday.
Rocks: Lincoln, Davies, Tomlinson, Tuck, Field, Charman, Whyte, Read, Smith, Muitt, Walsh. Subs: Block, Scutt, Wild, McCormick, Texeira.
Dorking: Huk, Philpot, Boulter, El-Abd, Taylor, McManus, Hall, O'Sullivan, Prior, Moore, McShane. Subs: Tolfrey, Sheridan, Beard, Sole, Beckles.
Ref: Jonathan Creswick