Cardiff will allow long-serving Kevin McNaughton to leave this summer along with Danny Gabbidon and Nicky Maynard.
Highly-rated Atletico Madrid midfielder Saul Niguez has signed a new five-year contract.
Seaborne has won three and drawn one of the four matches he has played in since making the temporary move to The Valley.
The 25-year-old was forced to sit out the final match of his original loan spell, last Saturday's 2-2 draw against Brighton.
But Seaborne will get the chance to extend his unbeaten run in the Charlton team after a fresh deal was struck.