Rea is deputising for the injured Casey Stoner in Honda's MotoGP line-up until the world champion is fully recovered from surgery on his Indianapolis crash injuries.
The Briton finished eighth on his MotoGP debut at Misano last weekend, and been linked to the last remaining prototype seat in the 2013 field at the Gresini Honda squad.
But instead Honda has announced that Rea will remain part of the Ten Kate line-up in World Superbikes for a fifth season.
"I'm happy to continue my partnership with Honda in this exciting championship," said Rea.
"I've been loyal to Honda my whole career and that's because I believe in them as a company and I believe that we can achieve more together in the future."
Rea is expected to remain on the MotoGP Honda for the next three races before Stoner returns for his home round in Australia.
Alongside his MotoGP commitments, Rea is also contesting the remainder of the WSBK season, where he currently holds fifth in the championship.
The two calendars do not clash for the rest of the year.