Approaching the match as clear favourites having won the last two editions of the tournament in Kolkata and Guwahati, Bengal received a rude shock in their tournament opener.
Maharashtra scored through Kailas Patel (20th minute) minute and L Machndo (70th) to go 2-0 up before Bengal reduced the margin through T Ahmed a minute later.
Bengal were seeded in the quarters, while Maharashtra made the grade by emerging champions from Cluster IV of the pre-quarterfinals, where they beat Arunachal Pradesh and Jammu and Kashmir.
The format of the Santosh Trophy has been altered this year with four groups of four teams each at the quarterfinal stage, with only the group toppers progressing to the semifinals.