Brentford confirmed the exit of Smith to Championship rivals Aston Villa on Wednesday evening, leaving the club to search for a replacement during the current international break.
This could affect Mokotjo, who is currently preparing for Bafana's 2019 Africa Cup of Nations qualifying double header against Seychelles.
The 27-year-old will now have to impress whoever takes over the helm in the coming weeks, which could either see him gain favour or fall down the pecking order.
The former FC Twente star arrived at the London outfit at the start of last season, and established himself as a regular in Smith's setup as he managed 29 starts and 10 sub appearances in 49 league and cup matches.
This season has seen Mokotjo used more sparingly, having managed just five starts and eight sub appearances in their 15 league and cup matches thus far.
With a new manager set to arrive soon, it is still to be seen whether he could play a more prominent role in the side or whether he may have to bide his time lower down the pecking order, depending on the coach's preferences.