Australia's lack of top-order runs has been a key reason in their falling 3-0 behind against England in the five-match Ashes contest ahead of the series finale at The Oval in south London.
After Australia's 74-run defeat in the fourth Test at Chester-le-Street on Monday, which featured their latest collapse, coach Darren Lehmann warned the batsmen they were playing for their places.
Khawaja, who has managed just 114 runs in six innings at an average of a mere 19 against England this Ashes, was clearly one of the players in former Australia batsman Lehmann's sights.
Unfortunately for the 26-year-old Pakistan-born left-hander, he could only manage four at Northamptonshire's Wantage Road ground on Saturday before he was caught behind off promising Durham all-rounder Ben Stokes.
Meanwhile Ed Cowan, looking to revive his international career, was caught behind off Liam Plunkett for 17 made in 47 balls while Phil Hughes, also trying to break back into the Test fold, was out for 30 when he played on to Keith Barker.
This match was originally due to involve Northamptonshire but the Lions were drafted in after the county club qualified for English domestic cricket's Twenty20 finals day.
But given the tour fixture remained a two-day contest, it was always going to be tough for Australia to achieve the morale-boosting victory they would have wanted following a winless run of seven defeats in their last eight Tests.
No Australia batsman made a fifty on Saturday after the Lions declared on their overnight 269 for seven, featuring Gary Ballance's 104.
However, all-rounder Shane Watson, leading Australia in the absence of rested captain Michael Clarke, made 45 and reserve wicketkeeper Matthew Wade (38 not out) and James Faulkner (29 not out) were unbeaten when bad light stopped play after tea with the tourists 227 for six.