A spokesman for HM Coastguard said nothing had been found during extensive searches and crews were stood down at 11:30 GMT.
The missing man has been named by police as Len King, 74, from Alfriston, East Sussex.
A friend reported him missing when he did not return home on Sunday evening.
Mr King had set out to sail alone from Brighton to Newhaven.
His Sunseeker yacht is believed to have been on autopilot when it drifted back to the marina and crashed into a wall with no-one on board.
Three lifeboats and a coastguard helicopter were involved in the search, which began shortly after 22:00 on Sunday.
It was hampered by storms overnight but resumed at first light in rough seas.
In a statement issued through Sussex Police, Mr King's wife Stephanie said her husband had been sailing since he was at least 20.
She said: "Normally we go together but during the week, if it's calm weather, he may go off by himself."
Mrs King said he went off just before lunch on Sunday and had been expected home by dinnertime.
When she phoned him several times the phone was unable to connect.
"I can't understand what has happened," she said.
"He is a very experienced yachtsman. He has all his equipment doubled up and is always careful. That is the way he runs things."
HM Coastguard said extensive shoreline searches had been carried out around Brighton Marina, between Shoreham and Newhaven and as far out as 2.5 miles off shore.
The helicopter had undertaken a search out to mid-Channel.
"Despite these extensive searches, nothing has been found. Unless any new information comes to light, the search has been suspended," a spokesman said.
Coastguards told BBC reporter Jon Hunt divers would examine the vessel to see if there was any mechanical explanation for what happened.
Insp Roy Apps said it remained unclear what had happened to Mr King.
He said: "The search is currently suspended and we are liaising with his family as we investigate the circumstances of his disappearance."
The search for the skipper of a yacht found abandoned near Brighton Marina has been called off and a missing person inquiry is under way.