The Blues were leading through the first of Didier Drogba's two goals when Malouda elbowed Ricardo Rocha, leaving the Portsmouth defender with a suspected fractured cheekbone.
The France international somehow escaped with only a caution before netting twice in 10 minutes at the start of the second half to wrap up a win that moves Chelsea to within a point of champions Manchester United.
Chelsea were in control almost from the first whistle and rarely needed to be at their best to see off a Portsmouth side - managed by former Stamford Bridge boss Avram Grant - already resigned to relegation to the Championship.
Home goalkeeper David James produced a fine flying save to keep out Frank Lampard's 25-yard pile-driver on 10 minutes.
James did not cover himself in glory as Drogba opened the scoring with the easiest of the 30 goals he has scored this season.
There seemed little danger when James came out to meet Deco's flick on but the ball bobbled under his foot as he attempted to clear, allowing Drogba to race through and tap the ball into an unguarded net.
Malouda's reprieve came five minutes before half-time when referee Lee Mason opted only to produce a yellow card despite seeing Rocha taken off on a stretcher.
Portsmouth's anger increased when Malouda doubled Chelsea's lead in the 50th minute.
Malouda raced beyond makeshift right-back Hayden Mullins before planting an unstoppable left-foot shot across James and into the top left corner from an acute angle.
The former Lyon star rubbed salt into Pompey's wounds on the hour mark.
Lampard's ferocious long range shot was beaten away by James only for Malouda to slam the rebound into the roof of his net.
Drogba claimed his 30th goal of the season in the in the 77th minute, latching onto John Obi Mikel's pass before outpacing Steve Finnan and drilling past James at his near post.
There was still time for Lampard to tap in Chelsea's fifth from Drogba's knockdown in the dying seconds.