The tourists, following-on, finished on 537 for nine after being bowled out for just 192 in reply to England's first innings 551 for six declared here at Lord's.
But their 14-hour resistance, which featured a fine century from captain Mahela Jayawardene (119) as well as battling fifties from Tillakaratane Dilshan (69), Nuwan Kulasekara (64) and Chaminda Vaas (50 not out), was aided by a series of fielding errors.
The most costly was when Andrew Strauss floored a routine slip chance when Man of the Match Jayawardene, who'd top scored in his team's first innings with 61, had made 58 second time around.
However, Flintoff maintained morale was still intact as England headed into the second Test of a three-match series, set to start at Edgbaston on May 25.
"The mood in the dressing room is great," the Lancashire all-rounder, deputising for the injured Michael Vaughan, told reporters. "They are a good bunch of lads.
"We would have liked to have come out of this game as a win. But we've got a lot of positives coming out of it.
"Some young bowlers have come in and peformed well on the big stage," he said in a reference to debutant Sajid Mahmood and fellow quick Liam Plunkett, playing his first home Test.
"And the batters are firing," Flintoff said of an England innings where Kevin Pietersen equalled his Test-best score of 158, opener Marcus Trescothick made 106 and Alastair Cook, in his home debut, 89.
"So I don't think it's necessary for doom and gloom. We are going alright.
"We've played some good cricket and our confidence hasn't been dented. We still expect to win the series."
And he was not overly-concerned by England's catching malaise. "I'm not going to make an issue of it to be honest.
"If you look at the past, we are a good catching unit. I dropped one at slip and I'm not one of the worst people standing there."
There were times on Monday's last day when Flintoff appeared to be captaining by rote, his field-settings formulaic.
It also seemed as if left-arm spinner Monty Panesar was underused while Flintoff himself bowled 50 overs for the first time in a Test match innings.
But the 29-year-old hero of last year's Ashes series defended his approach.
"As captain, I did what I thought was best. You go with your instincts. It was tough but I'm enjoying doing it."
And with worries about the risk of Flintoff suffering 'burn-out' ahead of the Ashes series starting in Australia later this year and the 2007 World Cup in the Carribbean, he insisted his lengthy bowling stint was a one-off.
"I'm alright. I've got a few miles in my legs and I've got through a few (overs). I think that's an exception rather than a norm."
Meanwhile a proud Jayawardene said: "It was brilliant effort from all our guys, especially today (Monday).
"Vaas guided Kulasekara superbly throughout the innings," explained Jayawardene of the duo's Sri Lankan record ninth-wicket stand of 105.
And of his own performance he commented: "In the past it's been said that responsibility is a problem for me. But I think I've probably proved a lot of people wrong."
However, he stressed: "We have to realise we've escaped from a bad first innings performance. We can't win matches by only competing for two days."
He added: "We have to get England out twice. We only got six wickets in this Test match," added Jayawardene, whose team now have a four-day warm-up game against Sussex starting Thursday before the second Test.
During the Lord's match former captain Sanath Jayasuriya arrived in England, the veteran opener now available for selection at Egbaston following his recent announcement that he'd ended his Test retirement.
"It's always good to have experienced heads in the team," maintained Jayawardene. "It gives us more options and is definitely good news for us."
England are due to announce their Edgbaston squad on Sunday.