Saturday's win preserved City's eight-month unbeaten record at St Andrew's and they are on course to finish in the Premier League's top 10 after being written off in pre-season as relegation certainties.
An own-goal from Burnley goalkeeper Brian Jensen broke the deadlock and Benitez's moment of glory came four minutes before the interval to wrap up the points. Steven Thompson scored a late consolation for the Clarets.
It remains to be seen whether Benitez will be at Birmingham next season with McLeish still to decide whether to take up the option to sign him permanently from Mexican club Santos Laguna.
Birmingham, who ended an eight-game run without a win, effectively made sure of top-flight football for another year a couple of months ago.
A mixture of experience - as epitomised by Barry Ferguson and Lee Bowyer - and players unproven at Premier League level like defenders Roger Johnson and Scott Dann, has been the bedrock of their success.
But Burnley, who were promoted alongside them from the Championship, have much rebuilding to do this summer to make an instant return to the Premier League.
Birmingham came close to taking the lead within the first 60 seconds. Cameron Jerome did well to create space for himself before sending over an inviting cross for Bowyer but, from six yards out, he headed wide.
The home side looked the more threatening and Benitez was put clear by Jerome after good play by Gregory Vignal.
But he hesitated over his shot and fit-again Burnley skipper Steven Caldwell was able to put in a saving tackle at the expense of a corner.
Jerome twice came close to breaking the deadlock in the space of 60 seconds.
First he headed over at the near post from a McFadden corner when unmarked and Jensen then parried away a close- range effort from the former England Under-21 player after he was teed up by Benitez.
Blues continued to look dangerous but it needed an own-goal from Jensen to give them the lead after 29 minutes.
Bowyer glanced a header across goal from Sebastian Larsson's cross which Jerome got on the end of in the six-yard box, but it needed a deflection off Jensen to ensure it crossed the line.
Four minutes before half-time Benitez scored his first goal at St Andrew's to double Birmingham's lead.
Caldwell brought down Jerome to the right of the Burnley box and a deep McFadden free-kick was headed back across goal by Johnson before Benitez applied the finishing touch at close range.
Burnley began the second half on the offensive and top scorer Steven Fletcher was only just too high with a powerful 25 yard drive.
Hart then needed two attempts to keep out a fierce drive from Fletcher.
Danny Fox became the first player to be booked after 50 minutes for a late challenge on Bowyer, who needed extensive treatment but was able to continue.
Blues looked lethargic but it needed a good tackle by Leon Cort to halt Jerome inside the box after he had been sent clear by McFadden.
The home side came to life and Benitez was only inches wide with a skidding low shot. Benitez's cross then picked out the run of Larsson who volleyed just wide when completely unmarked.
Stuart Parnaby became the first Birmingham player to be booked for a foul on Cork and Gregory Vignal followed him into the notebook for a late tackle on Tyrone Mears.
It then needed a block from Cort to deny Benitez his second goal of the game.
Stuart Parnaby was injured in a tackle by Fox and replaced by Keith Fahey with 11 minutes remaining.
Substitute Steven Thompson then pulled a goal back with three minutes left, clipping the ball past Hart into the corner of the net.