A frenetic opening quarter began when Marius Zaliukas headed in Ian Black's corner in the opening minute before the defender was sent off for tripping the excellent Paul McGowan 11 minutes later.
McGowan equalised from the penalty spot and Steven Thompson headed Saints' second after 19 minutes before Skacel found his range.
The Czech midfielder, whose contract is set to expire at the end of this month, equalised with a fierce shot after 23 minutes, struck his second after 64 minutes and a third after 69 minutes to enhance his bargaining power in negotiations - or for a move elsewhere.
Striker John Sutton, who was linked with a return to Paisley earlier this week, added a fifth in the final minute following an indirect free-kick in the area to complete the win.
Referee Steven McLean's decision to award the penalty and show Zaliukas a straight red card is sure to provoke further discussion, even though Hearts prevailed to go third in the standings above Motherwell, who lost 1-0 to Inverness.
The Buddies, meanwhile, are now without a win in four matches, since the defeat of SPL defending champions Rangers.
Hearts' recent unbeaten run has come since the first-team squad instructed players' union PFA Scotland to make a formal complaint following three successive months of delayed wages.
January's salary is due on Monday and should Hearts again fail to pay their squad on schedule, disciplinary proceedings would be triggered with the prospect of unlimited sanctions.
A burden had been lifted since the complaint was lodged, with Hearts playing with a freedom which has now delivered 15 goals in six games.
It took Hearts 84 minutes to break down Ayrshire juniors Auchinleck Talbot last week, but today they claimed the lead after 51 seconds.
Scott Robinson forced a corner and Black's set-piece found Zaliukas unmarked six yards out in the centre of the goal to head in.
Saints were awarded a penalty and Zaliukas was sent off after 12 minutes.
Kenny McLean's delightful ball over the top found McGowan, who was tripped when through on goal by last man Zaliukas as Marian Kello fielded the ball.
The Saints striker netted before gesturing to the incensed Tynecastle crowd, earning a booking and thus avoiding disciplinary proceedings at the hands of the Scottish Football Association's compliance officer.
The Buddies took the lead when Marc McAusland's cross from the right found Thompson, who beat Adrian Mrowiec to the ball and lofted a header over Kello.
Hearts equalised after the visitors failed to clear a corner, Skacel barging Jeroen Tesselaar off the ball and unleashing a fierce shot from 25 yards to score.
The tempo of the game began to slow as the pace of the opening period caught up with both teams.
Black was booked for an attempted trip on McGowan and Hearts boss Paulo Sergio was spoken to by referee McLean after leaving his technical area to protest against the decision.
Kello parried a Graham Carey drive from the left edge of the box before Skacel restored Hearts' lead.
Jamie Hamill's long throw found Sutton, who laid the ball off and Skacel made space before firing a shot into the bottom corner.
Five minutes later Skacel completed his hat-trick.
Black won the ball and Skacel struck another effort from the edge of the area which beat Craig Samson.
St Mirren brought on Nigel Hasselbaink up front and forged forward, but Hearts absorbed the pressure.
Samson unwittingly conceded an indirect free-kick in the box after Tesselaar attempted to control a ball into the box.
From six yards out, Black found Sutton, who drove the ball into the roof of the net to gain just reward for his efforts up front.