Sjoeke Nuesken and Guro Reiten gave Chelsea the lead before Alba Redondo pulled one back for the visitors before half-time.
Paulo Fonseca acknowledged that, despite their misfortune from the penalty spot, his team were deficient in several areas.
Ruben Amorim has been on the radars of several clubs including Liverpool, Chelsea and Manchester City.
Coming off the bench in the 57th minute, Chhetri bagged a brace to become the joint-highest goal-scorer in the ISL, level with Bartholomew Ogbeche on 63 goals.
While the secretive country's men's football team are currently ranked down at 111th in the world, their female counterparts have won two youth World Cups in two months.