Tanzania took the lead in the 39th minute when Cyprian Kachwele finished from inside the box after a quick counter-attack, with Feisal Salum providing the assist.
Madagascar responded strongly after the interval and equalised five minutes into the second half.
Nicolas Fontaine found the top corner with a left-footed effort in the 50th minute after being set up by Ehsan Kari, restoring parity for the Barea.
Neither side could find a winner during the remainder of the match, ensuring the points were shared.
Match details
• Madagascar: Nicolas Fontaine 50'
• Tanzania: Cyprian Kachwele 39'
Madagascar had the greater share of possession and registered four shots on target, while Tanzania managed one. Tanzania goalkeeper Yona Geoffrey also made several saves to keep his side in the contest.
The result gives both teams their first point of the qualifying campaign. Tanzania, however, are already guaranteed a place at AFCON 2027 as one of the tournament's co-hosts alongside Kenya and Uganda.
The other Group L teams, Nigeria and Guinea-Bissau, also met on Tuesday in the second round of qualifying.