On a pitch in no way befitting the hosts' lofty standing on the table, Wellington got off to the worst possible start. After some bright opening passages the Phoenix backline were caught on the counter in just the third minute when captain Alex Brosque picking out Rhyan Grant for a far post header that gave Glen Moss no chance.
Roy Krishna was unlucky to go into the book for a challenge on Michael Zullo that replays suggest was a clash of heads, before a fine passage of play ended with Tom Doyle looping a header over.
But it was Grant again at the heart of things in the 21st minute as Milos Ninkovic evaded his markers to start a flowing move, which Sydney's right back then whipped in for Bobo to nod home and double Sydney's lead.
Krishna was denied a fine header of his own in the 30th by the sharp reflexes of Danny Vukovic, but from Gui Finkler's resulting corner a terrific instinctive flick from Alex Rodriguez was deflected into the Sydney net by Vukovic to give Phoenix players a boost.
Inside a minute it was almost 2-2 as Kosta Barbarouses' mazy run finished with a shot that rolled just inches wide of Vukovic's right post, as Phoenix looked to run out the half the stronger side.
Moss then marked his 200th A-League appearance with a worldclass fingertip save from Joshua Brillante's rocket shot, to draw an entertaining first half to a close.
Hamish Watson came on for Michael McGlinchey for the second stanza and he was quickly in the action, hustling the Sydney defence to win a corner.
It was Wellington looking the brighter starters and Rodriguez could have had an unlikely second from another corner, but with Phoenix pressing it was the mercurial Ninkovic who capitalised on a poor turnover.
The Serbian received the ball to feet about fifteen yards out and placed a calm shot into the corner of Moss's net.
Matthew Ridenton came on in place of Jacob Tratt, but it was down the opposite flank that Phoenix almost pulled one back. A swashbuckling run from Doyle ended in a fine cross and Watson climbed above Alex Wilkinson, but his headed effort couldn't quite test Vukovic.
A flying run from Krishna ended in a booking for Wilkinson, creating a good set piece chance, but Finkler's freekick was well defended by the wall.
Phoenix pushed to get something from the game, but it was Sydney FC who were able to close out proceedings.