In a game that was closely contested in midfield, a Mohamed Larbi (43rd minute) spot-kick seemed to have given Mumbai City all three points. But an injury-time penalty from Stankovic (90+4th) ensured Hyderabad salvaged a point at home.
The victory helped Mumbai rise to fourth in the league standings with 23 points from 15 games and stay in reckoning for a play-offs berth with three more games left.
Mumbai City FC and Kerala Blasters continued their winless streak as they played out a 1-1 draw in an Indian Super League encounter.
Mumbai upped the ante and started creating a few chances after going behind.
A late goal from Amine Chermiti saw Mumbai City FC stun Kerala Blasters FC 1-0 in a closely-fought Hero Indian Super League clash at the Jawaharlal Nehru Stadium, in Kochi, on Thursday.
FC Goa returned to winning ways and rose atop the Hero Indian Super League table after 4-2 rout over Mumbai City FC, in Mumbai, on Thursday.
Both the teams gave it their all to find the winner but could not do so.
All the results from the I-League and ISL matches played on Saturday.