After just four minutes, a left-wing corner struck Victory captain Toivonen on the arm. Following a review on the pitch-side TV screen, referee Adam Kersey pointed to the spot and Mexican playmaker Ulises Davila coolly converted his third goal of the season.
The early goal allowed Wellington the luxury of sitting deeper and soaking up the inevitable opposition pressure.
Indeed, the home side enjoyed the greater share of possession, but the Phoenix's defensive system proved watertight, with Alex Rufer and Matti Steinmann playing crucial spoiling roles in front of the back four anchored superbly by captain Steven Taylor.
Victory's best first-half chance came from Danish midfielder Jakob Poulsen who saw his low drive repelled by a strong right hand from Stefan Marinovic.
The theme continued in the second half, with Victory searching for an elusive equaliser.
As frustration grew in the stands, Toivonen headed wide with the goal at his mercy just before the hour mark, but five minutes later the classy Swede scored a superb goal, jinking past two defenders in the penalty area before fashioning a sublime finish beyond Marinovic with the outside of his right foot.
Phoenix coach Ufuk Talay was forced into a late change with English striker Gary Hooper scratched from the matchday squad after picking up a quad injury in training.
Left-back Liberato Cacace returned from his two-game ban while there was a starting debut for Tim Payne in place of injured right-back Louis Fenton.
There was also a tactical tweak with Davila playing centrally as opposed to the wider role he has fulfilled in the first month of the season.
In the dying moments, Rufer had the chance to win Wellington the game in spectacular fashion, but saw his curling left-footed effort clawed away by Victory goalkeeper Lawrence Thomas.
The Phoenix have a bye next week and face Brisbane Roar at home on November 23.
Wellington Phoenix 1 (Davila pen)
Melbourne Victory 1 (Toivonen)
