It was reported earlier this week that Pompey were closing in on a deal to sign the former Republic of Ireland Under-21 international, who was out of contract at Ashton Gate.
The Robins were entitled to a compensation payment for the 23-year-old as he was offered a new deal and the matter was heading for a tribunal.
But earlier this week City agreed a compensation fee with Rotherham after signing 23-year-old striker Ryan Taylor.
And they have now ensured they do not have to go a tribunal over Henderson either, with both fees to remain undisclosed.
"We feel we've got fair deals on both players," City chairman Colin Sexstone told the club's official website.
"As much as possible you look for good value and I believe we've managed that."
Henderson made just five appearances for the Robins after joining them following his release by Aston Villa in 2007.
He was sent on loan to York, Weymouth and Aldershot before playing 33 games on loan at League One Yeovil last season.