The 30-year-old's previous deal was due to expire this summer, but he has now penned a contract extension, which will run until June 2015.
"I want to thank the club for giving me the chance to continue in this family. I'm very happy," he told reporters at a press conference.
"I wish we could continue with everyone from last year, that would be perfect, but the market is open and football takes many turns.
"We are in a project with an ambitious young coach who wants to contribute to the club, with enthusiasm and willingness to work. I just hope we don't suffer so much like last year. I'd like to retire at Malaga, but it will depend on how I play."
Eliseu joined Malaga from Lazio in 2010.