Fans of the band attacked festival boss Melvin Benn for choosing to let Allen take over the group's slot after the band pulled out of the Suffolk event - and many took aim at the Smile singer on Twitter.
Preparing to take the stage, Allen confessed she was "exhausted by nastiness" on Twitter, but she was in good spirits for her performance, even covering Two Door Cinema Club's Something Good Can Work and telling the crowd: "I'm sorry I'm not Two Door Cinema Club but I've promised I'll give it my best."
Benn later told reporters he was thrilled Allen had agreed to fill in: "She's done a fantastic thing in offering to come and play. It's a tough thing to find a headline act at the last minute.
"She's not been to Latitude before. I've spoken to her, she's very happy, (but) she's p***** off about the abuse from the Twitter cranks."
Allen also performed a brief set on another stage at the festival earlier in the day, and during her main performance, she brought her two-year-old daughter Ethel out with her and allowed the youngster to sing briefly for the crowd.
The Black Keys and Damon Albarn will headline the other two nights of the festival.