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Mikael Stahre also said he was shocked that his side failed to score.
FC Goa's Boris Singh scored the solitary goal in the 40th minute in Kochi.
Marquez will also manage FC Goa in 2024-25 before taking up the full-time job.
The 30-year-old had 29 goals and 16 assists to his credit from 54 games over the last two seasons for FC Goa.
City won the two-legged tie 5-2 after a 2-0 win in the second.
Chhangte scored two of City three late goals in a 3-2 win at Fatorda.
While Goa's first goal by Noah Sadaoui was a product of a proper team effort, the other one by Brandon Fernandes was one of the most sensational solo strikes of the season.
The Gaurs round off their league campaign with 45 points from 22 matches. They are thus level on points with Mohun Bagan Super Giant who play Mumbai City FC on Monday.
Chennaiyin FC are peaking at the right time and they now stand at 27 points from 21 matches.
Noah’s treble was complemented with a late strike by Spanish striker Carlos Martinez as Goa moved to 39 points in the standings, equalling their nearest competitors Odisha FC and the Mohun Bagan Super Giant.
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