The 27-year-old striker, who began his career at Fratton Park, is to return to Swedish club Elfsborg for the remainder of the season.
Keene rejoined the struggling south-coast club at the end of January and made nine appearances, scoring one goal in a 3-2 defeat by Colchester.
His final appearance came as a substitute in Saturday's 2-1 win at Crewe - Pompey's first victory in 24 matches.
Caretaker boss Guy Whittingham now has a spot to fill in his squad.
He said: "We'll think long and hard about filling that space and whether we bring in another striker or promote one of our youngsters."