An injury-time penalty from Josh Chamberlain gave Berko a 2-1 victory for their second away win of the week.
Opponents Stotfold may be bottom of the table, but they gave Berkhamsted a fright in one of the few SSML Premier division games to be played on Saturday.
With wind advantage in the first-half, Stotfold adapted better to the soggy pitch, with several Berko players struggling to stay upright.
Berko had a few early sighters from Alex Campana and Chamberlain which went wide of the target.
However, it was the hosts who broke the deadlock in the 20th minute when a free-kick was headed across goal from the back post and after a few scrambles it was Joe Ryan who finally got the ball over the line with a close-range shot.
Stotfold keeper Matt Fallon pulled off a few saves to deny Campana and Sean Coughlan as Berko tried to hit back. Coughlan and Ollie Cox then shot wide but the leveller did not come before the interval.
Early in the second-half Jon Munday stumbled onto the ground while in his own box and his momentum took his hand to the ball. The hosts were incensed when it was ruled to be accidental and their penalty appeals denied.
Berko broke and won a corner which Campana took and found Max Farrelly whose header struck the crossbar.
With the wind behind them, Berko got on top in the second period, but were wondering if it was not to be their day. Campana put a Cox cross wide and Munday got on the end of another Campana ball but couldn’t finish. Campana set up Farrelly but this time a defender cleared off the line. Adiel Mannion stretched but a cross eluded him.
Berko boss Steve Bateman decided to bring on the cavalry of Ashley Morrissey and Matt Bateman, who have both been out injured recently.
It was Mannion who equalised with a composed finish after Campana released him in the penalty area.
Campana then just failed to reach a Morrissey cross at the back stick, while Bateman headed wide and Stotfold defenders just managed to keep out Morrissey as he ran down the middle.
Into injury-time and Bateman ran through several challenges as Stotfold tired and he was eventually brought down, giving the referee no choice but to point to the spot.
The hosts caused an inordinate delay as they protested the decision to the referee and his assistant. Eventually, after consultation among the officials and a yellow card shown to a Stotfold player, the referee stuck with his decision.
Chamberlain duly stepped up and calmly netted the spot kick for the 2-1 lead.
Berko played out the last few minutes to collect the three points for their second away win of the week, following their 1-0 triumph at London Colney on Tuesday night (see report below).
Leaders Welwyn Garden City also snatched late goals to beat Oxhey Jets and stay ahead of second-placed Berko in the table, after The Comrades had briefly regained the lead after the Colney match.
Berko line-up vs Stotfold: Carl Tasker, Jack Pattison, Josh Camberlain, Steve Hawes, Jon Munday, Max Farrelly, Alex Campana, Ben Bateman (Ashley Morrissey), Sean Coughlan (Matt Bateman), Adiel Mannion, Ollie Cox (Adam Mead).Subs not used: Dan Jones and Jack Stevens.
Berko are two points behind Welwyn, although the leaders now have three games in hand.
The Comrades have the chance to get back to the top of the table tonight (Wednesday) if they can win at Welwyn, when they play their third consecutive away match and their third game against Welwyn in 14 days.
On Saturday Berko will host eighth-ranked Hoddesdon Town, who recently brought in a new management team of James Halsey and Michael Bardel.
Berko’s development side visit Leighton Town on Saturday after the disappointment of their trip to Risborough Rangers being called off at the weekend due to a flooded pitch.
The under-14s are at Finchley West on Sunday morning.