Indian Premier League chairman Rajeev Shukla tweeted his displeasure and said, " ......It is unfortunate that a team owner is not able to watch an IPL match."
It was learnt that prior to the game, Khan went to the team hotel to wish the players.
The MCA had yesterday asked the local police station to prevent Khan from entering the stadium.
Khan was banned for five years from entering the MCA premises, including the Wankhede Stadium, by the association's managing committee, then headed by the late Vilasrao Deshmukh, after he was involved in a fracas with the security staff and officials of the cricket body following KKR's victory over MI on May 16 last year.
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Tonight's match was the first KKR outing in Mumbai after last year's incident.
Earlier in the day, the Bollywood actor found support from political parties -- Congress and MNS -- who had asked MCA to revoke the ban.
"Whatever happened (at) that time was wrong. The chapter is closed now. He should be allowed inside Wankhede Stadium. He is not a terrorist who should be denied entry," Raj Thackeray told reporters.