The Germany international was released by the Royal Blues from their training camp in Austria yesterday to enable him to travel to Hamburg, where he discussed terms on what is reported to be a five-year contract.
He was due back in Gelsenkirchen today to say farewell to his former team-mates before making the permanent move north.
"He has flown to Dusseldorf because he is preparing for a transfer to HSV," revealed Schalke coach Felix Magath on his club's website.
"It seems both parties have a verbal agreement. We now have to see if that gets put down on paper. I expect the transfer to go through."
The 26-year-old, who has been linked with Sunderland, was one of Schalke's biggest earners having only recently signed a new contract until 2014.
"I did not have any perspective for a regular place in the Schalke team in my favourite position," he explained to the Revier Sport newspaper.
"Therefore, I wanted to change clubs. Things are different at HSV.
"In Hamburg, they were looking for a central defender. I think that I can show off my strengths well here."
Given the club's financial worries, the opportunity to strike him from the wage bill and earn a transfer fee believed to be around 7.5 million euros was too great for Magath to turn down, particularly since he has signed two new central defenders in Christoph Metzelder and Kyriakos Papadopoulos this summer.
"We have plenty of cover in defence so this is an area where we can most easily compensate a loss," explained Magath.
"Heiko does not want to leave because he is scared of the battle for places, even though I cannot promise him a place in the centre of our defence.
"But it is also obvious that we will miss Heiko. He has a very good attitude, has always trained well and achieved a lot as captain of our team.
"If the financial situation had been better here, a transfer would never have been an issue."