The Brazilian was Formula Three champion last year and he secured back-to-back titles after finishing second at Yas Marina while French rival Isack Hadjar stalled on the grid in the season's final feature race.
Bortoleto finished the season with a total of 214.5 points to Hadjar's 192.
Paraguayan rookie Joshua Durksen, who also has German nationality, won Sunday's race.
Red Bull-backed Hadjar, who had gone into the final weekend only half a point behind, finished overall runner-up with Alpine F1's Estonian reserve Paul Aron third.
Bortoleto follows current F1 drivers Oscar Piastri, George Russell and Charles Leclerc as winners of back-to-back titles in the feeder series.
Mercedes driver Kimi Antonelli, who is replacing seven-time world champion Lewis Hamilton at the Formula One team next season, was ill and did not race. He ended the campaign sixth overall.
Britain's Oliver Bearman, who will be racing for Haas in 2025 after competing in three grands prix this year with Ferrari and the US team, ended up 12th overall.