It's the second time Tharanga has been suspended this year, after missing two matches in June's ICC Champions Trophy for the same offence of his side's slow over rate.
Sri Lanka brought in Dinesh Chandimal and Lahiru Thirimanne to the squad in place of opening batsman Danusha Gunathilaka and the suspended Tharanga.
The hosts lost Thursday's match by three wickets and trail India 2-0 in the series.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Christian Radnedge)
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