The defender was accused of tossing away the armband in a disrespectful manner during Saturday’s mauling.
Paul Caddis was made captain by acting boss Martin Drury in a switch before the game.
O’Connor said after losing the armband that he would support the decision.
But after taking it when Caddis went off injured he then removed it.
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He refuted any negative intentions as he explained to Bradford City’s official website: ‘Martin took charge of the team and made the decision to give Paul Caddis the captaincy, which I was completely supportive of.
‘I have worn the armband with a great deal of pride this season and am right behind any manager’s decision. My job never changes. I am here to give 100 per cent for Bradford City.
‘It has been brought to my attention by members of staff at the club that supporters are unhappy with me, after I removed the armband during the second half.
‘Paul (Caddis) came off injured and I put the armband on in the dressing room - at half-time. The stitching was coming away and I had just headed the ball away for a corner.
‘I was getting ready to defend the corner and took it (the armband) off. I put it in the goal.
‘It is ridiculous to suggest I did it for any other reason. I would never disrespect the club or the captaincy. I wouldn’t have put it (the armband) on if I didn’t want to wear it.
‘Most importantly, I wouldn’t disrespect the travelling fans who made the long journey to support us.’
Ben Close scored two, while Tom Naylor, Jamal Lowe and Gareth Evans also netted as Pompey fired life back into their chase for an automatic promotion spots.