Jamshedpur won 3-0 to finish top of Group C and enter the semifinals.
The Disciplinary Committee also directed Blastes to issue a 'Public Apology', failing which the total fine will be increased to Rs six crore.
The biggest fan group of Blasters has launched a hashtag campaign in support of the Serbian head coach.
Kerala Blasters fans were quick to remind Parth Jindal of controversial officiating when their teams clashed in the knockout.
After a thrilling 2-2 at the end of extra time, ATK MB prevailed 4-3 in penalty shootout.
The title clash between ATK MB and Bengaluru FC will be played in Goa on Saturday.
In a thrilling second leg of the semifinal, Bengaluru won 9-8 in shootout after the match was tied 2-2 on aggregate.
Manjappada pointed out that Vukomanovic's decision was the culmination of a number of poor decisions against the Yellow Brigade and was not an emotional one.
The second leg of the semifinal contest will be held at Kolkata on Monday.
Sunil Chhetri came on as a substitute and found the back of the net in the 78th minute to give the Blues a vital advantage ahead of the second leg in Bengaluru on Sunday.