Needing three off the final ball, visiting skipper James Faulkner bowled a front foot no ball before Mike Hussey hit the winning runs off the free hit to set up a meeting with Brisbane Heat on Saturday.
Big-hitting duo Cameron White and Brad Hodge blasted the Stars to 183-2 from 18 overs in the rain-affected clash.
White cracked 88 off 53 balls and Hodge bludgeoned an unbeaten 70 off 43 balls.
More rain meant the Scorchers had a revised target of 139 off 13 overs and Scorchers opener Herschelle Gibbs was forced to retire on seven due to a hamstring injury.
Shaun Marsh blasted 27 off an Alex Keath over to take them to 65-1 off six.
Marsh went for 68 off 40 balls in the 10th over before Hussey (21 not out off 12) and Adam Vosges (36no off 21 balls) guided them to an eight-wicket victory albeit with some help from Faulkner and Jackson Bird who dropped the retired Test batsman off the first ball of that final over.
Warne, who did not captain the side after being sanctioned earlier in the tournament for a slow over rate and therefore facing the prospect of missing a potential final for a repeat offence, did not bowl in the contest.
And the 43-year-old, who had returned from a one-game suspension following his ugly altercation with Marlon Samuels, instead faces the prospect of a second suspension.
A CA Statement revealed Warne could be handed a further one-game ban when he appears before a hearing at a date to be confirmed.
"Cricket Australia has today advised that Shane Warne has been reported for breaching CA's code of behaviour in tonight's KFC T20 Big Bash League semi-final between the Melbourne Stars and Perth Scorchers," the statement read.
"Warne is alleged to have breached Rule 5: Laws of Cricket and Spirit of the Game. On 5 December 2012, KFC T20 Big Bash League teams were sent a memo by Cricket Australia.
"Under the heading 'Over Rates', the memo stated that 'If a team's official captain is selected but not named as captain, this will be considered against the spirit of cricket and may attract a code of behaviour charge'.
"For tonight's match, James Faulkner was listed on the Melbourne Stars team sheet as captain and took part in the coin toss with Perth Scorchers captain Simon Katich.
"Warne had previously been issued with one strike for a slow over rate violation, with a second strike this season resulting in an automatic one-match suspension. The time and date of the hearing is yet to be determined."
Should Warne be banned it could provide a sour end to a controversial career that saw him take 708 Test wickets, a world record when he retired from international cricket following Australia's Ashes whitewash in 2007.