Phete, 25, joined the newly-promoted side in the off-season after four years with Vitória Guimarães in search of regular first-team football.
However, after arriving with an injury, the Stars of Africa academy graduate struggled to break in the first XI as they defied expectations and currently sit in fourth place behind Sporting Lisbon, Porto and Benfica.
As a result, Belenenses moved quickly to secure the services of the technically gifted centre-back to bolster their ailing defence.
"[Thibang] Cafú Phete is [our new] reinforcement until 2022," the club announced on Thursday.
"A powerful 25-year-old 1.87m player who can play both in midfield and in defence! Welcome Cafú."
Phete becomes the second South African at the club with Sphephelo Sithole (20) already within the ranks of the side managed by Portugal legend Petit.