Anand lost by identical 0.5-1.5 margins. After losing to Rauf Mamedov of Azerbaijan in the first round on the opening day on Saturday, the Indian chess ace could not register any win in his two matches on Sunday. He lies in sixth spot with two others.
India, which has qualified for the quarterfinals, will face France in the fifth and final preliminary match later on Wednesday.
The US will face Russia who got the better of China in Wednesday's finale.
12 year old Abhimanyu Mishra from New Jersey on June 30 scored his third GM norm and became the youngest chess grandmaster in history. He already crossed the required 2500 Elo rating barrier.
Mendonca, who achieved the feat at 14 years, 9 months and 17 days, is the second GM from the coastal state.
During normal times, state chess tournaments and others would have been held but it was not to be this year, the official added.
The top-seeded Indians, who were sixth after three rounds, were held to a 2-2 draw by a strong Kazakhstan team, seeded second, in the sixth round.
Te Indian chess team recently emerged joint champions (with Russia) at the recently-concluded FIDE online Chess Olympiad.
The Tamil Nadu player scored seven and half points out of a possible nine with six victories and three draws to finish on top, ahead of many higher-rated Grandmasters, a press release said on Thursday.
India won the chess Olympiad gold for the first time in the tournament's history and the team's skipper Vidit Gujrathi has revealed that this win is on par with how Indian cricket was put on the world map after their 1983 World Cup win against the West Indies in Lords.
The former world champion said "most Indian parents are right" that chess will help their children do better in school.
Vaishali registered a 6-5 win over Bulgarian opponent late on Wednesday after having beaten strong players like Valentina Gunina and Alina Kashlinskaya in the qualifying stages.
USA will meet China in Sunday's Superfinal after they beat the top seeds 2.5-1.5 in the final round later in the day.
India were held to a 2-2 draw against Europe in the Online Nations Cup Chess tournament.
Five-time world champion Anand was in Germany to take part in the Bundesliga chess tournament and before he could return, the travel restrictions came calling in wake of the COVID-19 pandemic.
British chess legend and FIDE (world chess federation) vice-president Nigel Short, who participated, said he was glad to be of help in the fight against COVID-19.
Secretary and convenor of the five-member panel Naresh Sharma took strong objections to Despande's recent statement against the decisions taken by the AICF general body meeting held online recently.
The 50-year-old reflected on sports in time of worldwide lockdowns and said chess seems to have coped well so far.
A total of 17 Grandmasters and over 180 chess players participated came together to take part in an online blitz event to raise over Rs 2.39 lakh towards the PM CARES Fund for COVID-19 relief.
Some young chess players from across the country hosted an online tournament and raised Rs 1.05 lakh while noted coach R B Ramesh collected funds through his 'Chess Gurukul' with GM P Harikrishna contributing Rs 2 lakh and Karthikeyan Murali donating Rs 25,000.
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