It was Boca's second successive defeat, and they are two from bottom with 11 points after 12 matches of the Clausura championship, 16 points behind leaders Independiente.
Simeone quit as San Lorenzo coach on Saturday after their 1-0 home defeat by Gimnasia-La Plata. San Lorenzo also have 11 points from 12 matches.
Boca's Argentina striker Martin Palermo said everyone at the club was to blame for the lowest ebb he has seen at the club, four times South American champions in the last decade, since his debut in 1997.
"Boca are not used to experiencing this kind of situation," he told reporters.
To add to Boca's woes, playmaker Juan Roman Riquelme was sent off after Central's winning goal four minutes from time, booked twice in quick succession by referee Rafael Furchi, apparently for dissent.
The winner was headed in by forward Milton Caraglio after Boca keeper Javier Garcia was caught stranded off his line trying to catch a free-kick.
WORST DEFENCE
Riquelme laid on the equaliser on the hour for striker Nicolas Gaitan after Adrian de Leon had put Central in front from defender Guillermo Burdisso's header just before halftime.
Boca, who not lost to Central at their Bombonera home since 1990, maintained their record as the worst defence, having conceded 24 goals at an average of two per game.
Godoy Cruz scored twice in a minute to beat Velez Sarsfield 2-0 at home in Mendoza and keep pace with Independiente, 1-0 winners against Arsenal on Saturday.
Independiente have 27 points from 12 matches and Godoy Cruz 24 with Argentinos Juniors third on 22 after Saturday's 2-1 win over Chacarita Juniors.
Estudiantes de La Plata, held 1-1 by title holders Banfield on Sunday, are fourth with 21 points.
Estudiantes lost striker Mauro Boselli, who headed their goal in the 14th minute, with a leg injury just before the interval.
He could miss their last Libertadores Cup Group Three match at home to Alianza Lima on April 20.
Estudiantes goalkeeper Agustin Orion saved a second-half penalty from Banfield's Uruguay forward Sebastian Fernandez with the score 1-1 following Marcelo Quinteros's 40th-minute equaliser.
Estudiantes substitute Enzo Perez was sent off in the 69th minute, six minutes after coming on, for diving, his second yellow card offence.
