The former Buddies captain is back as manager after replacing Oran Kearney but his first competitive game in charge saw the Pars spring a Betfred Cup shock.
Saints were a mess at the back as Ryan Dow, Andy Ryan and Tom Beadling all took advantage during a first-half blitz.
Cody Cooke and Danny Mullen did pull back two goals but it was not enough to prevent Stevie Crawford's Fifers storming to the top of Group H.
Goodwin was only appointed a fortnight ago and it was soon clear the Irishman's new side are still worryingly undercooked.
Ryan Flynn was stripped of possession out wide after 19 minutes and Pars pounced for the opener. Josh Coley swapped passes with Kevin Nisbet before sliding the ball through for Dow, who stroked home with a lovely finish.
Flynn was at fault again seven minutes later with a wayward pass and for the second time, the visitors countered without mercy.
Beadling knocked the ball to Nesbit who ghosted past Stephen McGinn before picking out Ryan on the move. Gary MacKenzie failed to get close and the striker made him pay as he found the corner of the net.
And Goodwin was left with his head in his hands five minutes before the break as Beadling darted past McGinn to fire home on the rebound after Ryan hit against the base of the post.
But the Buddies finally got their act together as the clock ticked past the hour mark.
Their first goal came after 63 minutes as Cooke's 20-yard strike took a nick off Beadling to take it past Ryan Scully into the corner of the net.
And they struck again within two minutes as Tony Andreu's back-post corner broke off Paul McGinn for Mullen to tap home.
Saints sent keeper Vaclav Hladky up in stoppage time but there were no last-gasp heroics as the Czech stopper headed wide.