The Asian Football Confederation (AFC) said in a statement late Tuesday that the winners of the glitzy tournament, which is backed by India's richest man Mukesh Ambani, will go into the continental competition's qualifying round.
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It said it had acted on a recommendation from the All India Football Federation (AIFF), which is grappling with how best to accommodate two rival leagues — the ISL and the older I-League.
"The Committee approved that the I-League champions will play in the AFC Champions League Play-off round and the ISL Champions will play in the AFC Cup preliminary stage... from 2018," read the statement.
The ISL, whose city-based franchise format apes cricket's hugely successful Indian Premier League, has grown in popularity since it was launched in 2014, outstripping the 10-year-old I-League in broadcast ratings.
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It is adding two new teams to this year's event, bringing the number of clubs to 10, including one side which has defected from the I-League.
Bengaluru FC, two-time I-League winners, and Jamshedpur will be the new franchises when the next season kicks off in October. They are backed by major companies — the Jindal South West conglomerate and Tata Steel respectively.
There have long been reports of a possible merger between the two competitions but the AIFF has played down such talk in recent months.
The AFC said in its statement that the ISL and the I-League will run simultaneously for six or seven months in 2017 and 2018 and that as a "short-term bridging solution" it was giving "special dispensation" to the ISL.
Italy's Alessandro Del Piero and French striker Nicolas Anelka are among the veteran former stars to have played in the ISL but local media reports say sides are starting to focus more on nurturing young Indian talent.
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