Ivory Coast left captain Didier Drogba out of the starting line-up but it was his arrival off the bench after an hour which coincided with the African nation finally converting their chances.
Japan’s star player Keisuke Honda had put them ahead with an impressive strike after 16 minutes and, as Ivory Coast continued to miss chance after chance, it seemed their bid to qualify for the knockout stages would take an early hit.
However, Drogba’s introduction gave their opponents something else to think about and, while they were doing that, Bony and then Gervinho both nipped in to convert crosses from right-back Serge Aurier – a reported transfer target for Arsenal after they lost Bacary Sagna to Manchester City this week.
AC Milan midfielder Honda had given Japan the lead, drilling a shot inside a stationary Boubacar Barry’s right-hand post.
Atsuto Uchida should have made it 2-0 after cutting in from the right but opted to go for goal and shot straight at the goalkeeper with team-mates well placed in the middle.
Ivory Coast, with Manchester City midfielder Yaya Toure captaining the side but plainly not at his best after recovering from a hamstring injury, stepped up the pressure but failed to test goalkeeper Eiji Kawashima, with Salomon Kalou heading over from six yards just before the break.
Either side of Bony making a mess of two headers early in the second half, Toure appeared to be brought down by Maya Yoshida but no penalty was awarded.
With frustration growing, Drogba was introduced and, within six minutes, his side were ahead. Bony equalised in 65th minute with a glancing header, before former Arsenal forward Gervinho beat Kawashima all too easily at his near post to stun the Japanese.