Drogba limped off after a high 15th-minute challenge by Japan defender Marcus Tulio Tanaka.
Two minutes earlier, Drogba's 22-meter (24-yard) free kick was deflected by Tulio into his own net.
Defender Kolo Toure scored from close range in the 81st, meeting a free kick with a crisp shot.
Japan's fourth straight defeat included more own-goal trouble. It conceded two in a 2-1 loss to England last Sunday.
With just two official warm-ups to prepare for the World Cup, Ivory Coast coach Sven-Goran Eriksson stuck with the same tactics he used against Paraguay in a 2-2 draw last Sunday.
A 4-3-3 formation had a central axis pairing Kolo Toure in defense with career midfielder Didier Zokora, Yaya Toure anchoring midfield and Drogba the focus in attack.
The Ivorians' blend of muscle and skill soon gave problems for Japan, which conceded a free kick when Aruna Dindane went down theatrically.
Drogba's shot took two deflections, the second off Tulio, to deceive Japanese goalkeeper Eiji Kawashima and bounce slowly into the bottom right-hand corner of the goal.
Two minutes later, Drogba and Tulio clashed in the air as the Ivorian captain flicked the ball over the defender's head.
Drogba refused the offer of a stretcher and limped off to be replaced by Seydou Doumbia.
Doumbia soon impressed, lashing a long-range shot just over the goal and going close with another 20-meter (22-yard) drive in first-half stoppage time.
Japan made three midfield changes for the second half, and free kick specialist Shunsuke Nakamura forced 'keeper Boubacar Barry into a diving save in the 49th.
In the 61st, an alert Yasuyuki Konno cleared the ball as Doumbia seemed poised to strike from close range.
Ivory Coast made the game safe with a second goal in the 81st.
A long free kick from the right flank was met on the half-volley by Kolo Toure with 'keeper Kawashima rooted to his goal line.
Ivory Coast's World Cup opener against Portugal is June 15 in Port Elizabeth. Their Group G also includes Brazil and North Korea.
Japan begins Group E play against Cameroon on June 14 in Bloemfontein, then faces the Netherlands and Denmark.
Boubacar Barry, Guy-Roland Demel, Kolo Toure, Didier Zokora, Siaka Tiene, Emmanuel Eboue, Yaya Toure, Cheick Tiote, Aruna Dindane (Gervinho, 73), Didier Drogba (Seydou Doumbia, 18; Abdul Keita, 62), Salomon Kalou (Emmanuel Kone, 88).
Eiji Kawashima, Yasuyuki Konno (Yuichi Komano, 68), Yuji Nakazawa, Marcus Tulio Tanaka, Yuto Nagatomo, Keisuke Honda (Shunsuke Nakamura, 46), Yuki Abe (Junichi Inamoto, 46), Yasuhito Endo (Kengo Nakamura, 46), Yoshito Okubo (Takayuki Morimoto, 65), Makoto Hasebe, Shinji Okazaki (Keiji Tamada, 55).
