Malouda lost his place in the Blues' starting line-up but was brought on in the first half and came to the rescue by converting Jose Bosingwa's cross with seven minutes remaining in Saturday evening's Premier League clash at Stamford Bridge.
Villas-Boas had been heading for his first league defeat for more than 16 months when Shane Long continued his dream start to life at Albion by giving them a half-time lead but Nicolas Anelka equalised with a deflected shot before Malouda pounced.
But Chelsea looked anything but title challengers and are in desperate need of the type of midfield inspiration the likes of transfer targets Luka Modric and Juan Mata would doubtless provide.
Saturday's game looked a home banker on paper, with Chelsea having beaten the Baggies in all 10 of their Premier League meetings and thrashing them 6-0 in last season's corresponding fixture.
Villas-Boas, who did not lose in the league at Porto last season, gave a sheepish wave to his new supporters after taking his seat in the dugout but it took less than four minutes for reality to bite.
Bosingwa's pass put Alex under needless pressure from Long, the striker robbing the defender before bearing down on Hilario, whose first task deputising for the injured Petr Cech was picking the ball out of the net.
Chelsea were struggling to get in behind the visitors, who were having no such problem, with Paul Scharner testing Hilario from a tight angle.
And it should have been 2-0 in the 25th minute, a brilliant Chris Brunt ball releasing Long, whose cross was too far in front of Somen Tchoyi.
Frank Lampard was booked for an ugly lunge on Long 10 minutes before half-time, with Villas-Boas immediately abandoning Plan A by withdrawing Salomon Kalou for Malouda.
It took until the 41st minute for Chelsea to truly threaten, Ashley Cole unleashing a rising drive towards the top corner, which was tipped behind by Ben Foster.
The home fans screamed for a penalty two minutes later when Foster clattered into Anelka but referee Lee Mason felt the goalkeeper had got a bit of the ball.
There was still time for Youssouf Mulumbu to be booked for bringing Fernando Torres near the edge of the box but Alex's free-kick deflected off John Obi Mikel and through to Foster.
There was little improvement from Chelsea at the start of the second half but a slice of luck helped them equalise in the 53rd minute.
Lampard went down in the box laying the ball back to Anelka, who cut inside and unleashed a shot which took a telling deflection off the heel of Jonas Olsson and nestled in the far corner.
The goal sparked the game to life, Scharner heading James Morrison's cross over the bar and Malouda seeing a half-volley blocked before Lampard played in Anelka, whose shot hit the legs of Foster and rebounded to Malouda, only for Steven Reid to throw his body at the ball.
Torres, who was unable to repeat his encouraging performance of the previous week, was withdrawn for Didier Drogba just before the hour, with Olsson booked for dissent during the substitution.
Tchoyi's left-foot 25-yard curler forced an acrobatic save from Hilario and an under-pressure Drogba steered Cole's cross wide before Villas-Boas made his final change when Branislav Ivanovic came on for Alex.
Lampard and Anelka were linking up well, the latter hooking over under pressure before Drogba just failed to control a great ball from Ivanovic.
West Brom threw on Peter Odemwingie for Tchoyi for the final 15 minutes but Chelsea were applying the pressure and Cole's low cross-cum-shot was blocked by Foster.
There were more penalty cries when the ball hit the arm of Olsson, while Lampard lifted a half-volley over the bar.
Anelka wasted a great breakaway chance with eight minutes left, steering the ball into the sidenetting from 35 yards after Foster had come racing off his line.
It did not matter as the winner arrived a minute later, Bosingwa skipping too easily between Morrison and Nicky Shorey down the right and producing the ball of the match, swept home by Malouda at the far post.
Graham Dorrans came on for Mulumbu for the final three minutes and the unmarked Odemwingie could easily have equalised a minute later, his volley too close to Hilario.
The game ended with John Terry booked for a clash with Odemwingie, who was himself carded following a similar tussle with Cole.