The on-loan pair missed Saturday's 1-1 FA Cup draw with Bury having been denied permission by respective parent clubs Watford and Millwall to feature in the competition.
But they will be back to boost the Shrimpers as the Essex club aim to make it into the semi-finals.
One player who does miss out, however, is loanee Marc Laird who played earlier in the competition for Leyton Orient.
Manager Paul Sturrock had named the same starting line-up for five matches leading up to the clash against Bury at the weekend but, with Assombalonga and Mkandawire unavailable, he was forced to make two changes - striker Freddy Eastwood and midfielder David Martin coming in.
And it appears as though further changes could be on the agenda against Brentford.
Sturrock told the club's official website: "A couple of the lads picked up a few knocks on Saturday, and if the game was on Monday evening they certainly wouldn't be playing.
"We'll assess them on Tuesday but we're not going to risk anyone because we've got a lot of important games coming up throughout December.
"It will give a few of the lads the opportunity to come in and stake their claim for a place in the side though, and hopefully we'll see a reaction."