The striker, who had a loan spell with the Seagulls earlier in his career, capitalised on poor defending by Dan Harding to seal Stoke's third win on the trot and lift them into the Championship play-off zone.
There seemed no danger when Akinbiyi out-muscled Harding for the ball near the touchline halfway inside Brighton territory.
However, Akinbiyi then made progress into the penalty area to fire home his seventh of the season with a low left-foot drive in off a post from 12 yards.
It was another nightmare for Harding, the England Under-21 left-back who is being tracked by several clubs including Everton and Rangers.
Manager Mark McGhee blamed Harding for both of Milwall's goals in Albion's previous match and the Brighton boss substituted the youngster moments after his latest blunder.
The result was rough on Brighton, who had shown plenty of determination following the departure earlier in the day of captain Danny Cullip to Sheffield United for £250,000.
Brighton currently have a cash crisis and also sold midfielder Darren Currie to Ipswich Town last week.
They shrugged off the off-field turmoil with a spirited display. Mark McCammon made an encouraging debut after his one-month loan move from Milwall alongside the outstanding Leon Knight.
Knight thought he should have had a penalty midway through the first half when he went down under a challenge by Stoke defender Wayne Thomas after goalkeeper Steve Simonsen had mis-kicked.
Knight was instead booked for diving, his fifth yellow card of the season which rules him out of the vital home clash with Gillingham on Boxing Day.
Knight was also denied an early goal when Simonsen somehow kept out his header from point-blank range.