A pack of journalists were the only people to greet batsman Virender Sehwag and wicket-keeper Mahendra Singh Dhoni when they touched down at New Delhi's Indira Gandhi airport just before midnight.
Security personnel whisked both players from the terminal into waiting cars before the media could approach them.
Coach Greg Chappell, batting superstar Sachin Tendulkar, Ajit Agarkar, Munaf Patel and Irfan Pathan arrived in Mumbai a few hours later, where they were greeted by cricket board secretary Niranjan Shah and other officials.
Captain Rahul Dravid and his Bangalore team-mates Anil Kumble and Robin Uthappa also arrived home safely.
Former captain Sourav Ganguly was expected to remain in London for a few days. The travel plans of the remaining players were not immediately known.
Indian police, aware of the hostile protesters that greeted Pakistan's team on Wednesday, tightened security at airports and around the players' homes to prevent any incident.
"We want to ensure the players are not hassled," Mumbai's joint commissioner of police, Arup Patnaik, told reporters.
Angry fans had taken to the streets when India were knocked out of the first round at the ongoing World Cup in the Caribbean.
The Indian board has summoned Chappell, Dravid and former captains like Sunil Gavaskar and Kapil Dev for a meeting in Mumbai on April 6 and 7 to discuss the World Cup debacle.