Wellington started energetically, Roy Krishna drawing a save from Victory goalkeeper Lawrence Thomas inside the first minute. Their ascendency continued for the first quarter of the game, zipping passes across the pristine surface and creating more chances than their hosts.
Mandi fired a 14th minute free-kick straight into the defensive wall and five minutes later released Krishna with a precise long ball, the Fijian bringing David Williams into play before Ryan Lowry directed his shot into the side-netting.
Rudan made six changes to the side that were humbled by Perth Glory five days ago, the most significant the return of Williams to his customary attacking role alongside Krishna, with Lowry handed just a sixth start of the season in the problematic right wing-back spot.
Cheered on by a raucous home crowd of 16,000, Victory grew into the game, Honda testing Filip Kurto with a dipping effort from distance before Toivonen dispossessed Mandi in the centre-circle and ran half the length of the field, eventually firing wide of the post.
The Phoenix's aggression often crossed the line, with Michal Kopczynski and Williams both booked in the first half. From the last of the dozen free-kicks Wellington conceded in the first stanza, Victory went ahead. Keisuke Honda curled a sublime ball towards the penalty spot and found Georg Niedermeier running untracked into the penalty area, the German defender cleverly steering his header past Kurto who had elected to stay on his line.
Seeking a way back into the game, Wellington made that task much harder for themselves just after halftime through their own carelessness. Toivonen seized upon a badly underhit back-pass from Mandi and fed Kosta Barbarouses who slotted coolly under the advancing Kurto to notch his 15th goal of the season and double Victory's lead.
Rudan immediately introduced Sarpreet Singh whose impact was instant, crossing deftly for Krishna to steer home his 19th goal of the season and throw Wellington a lifeline after 64 minutes. Singh's influence was noticeable, the young kiwi finding space between Victory's lines as Wellington looked for an equaliser.
But Toivonen snuffed that hope out with a superb third for Victory, sprinting after a through ball from Barbarouses which Kopczynski tried vainly to clear, advancing towards Kurto and producing a delightfully dinked finish from the narrowest of angles.
Tempers flared in added time, with Kopczynski sent off for a second yellow card and given a parting shot by Victory coach Kevin Muscat who, along with Phoenix assistant coach Paul Gothard, was also booked in the resulting exchange.
The defeat spells the end of Rudan's tenure in Wellington and he is expected to shortly be confirmed as the coach of the A-League's newest club, Western United.
But he was in no mood to look ahead in the immediate aftermath of his side's exit.
"I'm focused on my players and my football club and not winning," said Rudan.
"I firmly believed, as did my players, that we would have another week. I'm bitterly disappointed for my players, the club and the fans that we couldn't go one step further. We planned on playing Perth Glory next week. That's how I'm feeling right now."
Several Phoenix players are now off-contract with their futures to be revealed in the coming days.
Melbourne Victory 3 (Niedermeier 42', Barbarouses 53', Toivonen 71')
Wellington Phoenix 1 (Krishna 64')
