Eagles took the lead at the Peter Mokaba Stadium through a goal on 13 minutes by Siyanda Ngubo.
Baroka levelled thanks to Victor Letsoalo’s 34th minute effort.
NFD top scorer Thabiso Kutumela put the home side ahead a minute after the restart, but the KZN club ensured their trip north was not in vain when Ngubo completed his brace just after the hour-mark.
The draw means Baroka trail All Stars by one point after the Cape side beat Mthatha Bucks 1-0 on Friday.
Meanwhile, Mbombela United’s sparkling form continued as they moved to fourth spot with a hard-fought 1-0 win over Milano United.
Sifiso Thomo’s second-half goal was the difference on the day at the Kanyamazane Stadium outside Nelspruit.