A less-than-popular Clarke was roundly booed throughout his slow-paced innings of 36 off 57 balls in Sunday night's six-wicket one-day win, which even had surprised English rivals feeling for him.
While Shane Watson belted his side to victory with an unbeaten career-high 161, Clarke felt the wrath of MCG fans incensed by his efforts which heaped extra pressure on Australia's run-chase.
The stand-in captain scored just seven off the first 21 balls he faced, all singles, and the only four of his innings came courtesy of two separate overthrows.
Even with Watson blasting away, the run-rate required lifted from six an over when Clarke's innings began to a concerning 7.5 per over with 16 overs left chasing England's big total of 294.
Watson defended his captain, arguing he performed a creditable role in keeping wickets intact and seeing off the old white ball when it was reversing, making batting difficult.
"When the crowd is starting to boo a bit it's disappointing but the crowd doesn't exactly know what our game-plan is through that period," he said on Monday.
"It was a period we couldn't afford to lose another wicket - and Michael did a brilliant job to really set up the platform for the rest of the onslaught towards the end."
But England skipper Andrew Strauss admitted he'd never been subjected to such abuse from his own fans and paceman Ajmal Shahzad, who eventually caught Clarke as he unsuccessfully attempted to hit out in the 39th over, also said he'd never heard anything like it.
"To be honest with you I haven't," Shahzad said.
"It can only be good for us."
Clarke's poor form this summer, as Australia lost the Ashes series 3-1, and reports of his lack of popularity among teammates and the public have seen pressure grow on his standing as Australia's heir-apparent to Test and one-day skipper Ricky Ponting.
The 29-year-old dropped himself from the national Twenty20 team, despite being skipper, after the Ashes and doubts continue to grow over his ability against the white ball in the 50-over game.
However Clarke is certain to be included in Australia's World Cup squad which is set to be named on Tuesday, travelling to the sub-continent as Ponting's deputy.
Cricket Australia public affairs manager Peter Young said the amount of interest Clarke received from businesses looking for his endorsement proved his popularity.
Young said he believed Clarke would win more support as he emerged as a leader.
"Our view is that Michael is a sensational young man and is developing as a significant leader, and we're confident that over the fullness of time that his bat and leadership will speak for itself," Young said.
"He will become very popular."
Young felt part of the angst from a parochial Victorian crowd came from the fact local hero Brad Hodge had been overlooked for selection, highlighted by one fan jumping the fence and abusing selector Greg Chappell during a 1971 team lap of honour.
"Brad Hodge is remarkably popular in Victoria and he's a bit of a cult hero with their crowds," Young said.
With 15 players to be named for the World Cup defence and Ponting to return from a broken finger, most intrigue surrounds whether the selectors will keep two front-line spinners.
Both Nathan Hauritz and Xavier Doherty are in the current 14-man squad to play England and Hauritz was rested at the MCG to give Doherty an audition, which resulted in 0-40 from seven overs.