After high school, Mkhabela moved to Bloemfontein and made 10 appearances for the Free State U19 in 2013. In 2014, Mkhabela was selected in the SA U20 squad that participated at the 2014 IRB Junior World Championship in New Zealand.
Upon his return to domestic action in 2014, he played in 11 matches for the Free State U21's.
In 2015, Mkhabela was included in the UFS Shimlas squad for the 2015 Varsity Cup. He made seven appearances for the Shimlas in the pool stages but missed out on the play-offs. After the competition, Zee was named as replacement scrum-half in a Varsity Cup Dream Team that played a match against the SA U20’s
Mkhabela played in three Currie Cup matches for the Toyota Free State Cheetahs, making his debut on 8 August 2015 from the bench against the Blue Bulls.
Mkhabela made his SuperRugby Debut on the 25 Feb 2017 against the Lions.
Made his PRO14 debut 6 January 2018 against Benetton in Italy.