Bobo's 10th-minute strike, his ninth of the season, and an 83rd-minute effort from Kosta Barbarouses made sure of the points for Sydney.
It leapfrogs Central Coast Mariners into second, though the Mariners have a game in hand.
Further good news for Sydney came in Wednesday's later game, as fellow semi-final berth contender Adelaide United slipped up 2-1 at Perth Glory.
Kusini Yengi put Adelaide seemingly on course to join Sydney on 38 points when he converted at the far post in the 28th minute.
But Bruno Fornaroli scored for the fifth straight game against Adelaide, heading in a 78th-minute equaliser from Chris Ikonomidis' excellent right-wing cross.
And it was Ikonomidis who completed the turnaround in style, lashing home from Fornaroli's volleyed cross across the area after good work from Nicholas D'Agostino.
Having lost a game in which they dominated possession, Adelaide stay fourth, while Glory are now level on points with sixth-placed Brisbane Roar in the race for the last quarter-final spot.