“It was a game we could’ve won,” Heath said afterwards. “It was a tough pitch, it was bobbly and hard, but the boys played the conditions well for the first 40 minutes. The biggest lesson for us will be that we’ve got to take our chances.”

Blues made two changes to the team that had been held to a goalless draw by Milton Keynes Dons a fortnight earlier, with Bobby Unwin making his first start for four months in place of Tayo Adedoja and Charlie Sayers making his competitive U18s debut for the club instead of Mitchell Fallows at left-back.

Unwin has endured a difficult season with injuries, but he was involved in this fixture from the start and in the fifth minute he saw a free-kick charged down before Oli Coker’s follow-up was also cleared to safety by the Northampton defence.

Six minutes later Southend went even closer to the opening goal after good hold-up play by forward Tendi Quamina. He found Coker, whose first-time pass was collected by Cameron Brown on the left-hand apex of the penalty area. He cut inside and turned Max Dyche before curling his shot against the top of the crossbar.

On 21 minutes the visitors took the lead, Demaray Anyadike winning the ball in midfield and immediately sprinting forward to hang a cross up to the back post, where Unwin powerfully nodded down and into the net. It was just a second goal of the campaign for the winger, and the 13th of his youth team career.

Blues were frustrating their opponents, refusing to give them any time on the ball and then turning them around quickly to cause them trouble at the back, although midway through the opening period Collin Andeng Ndi was called upon to make a tumbling save to keep Southend in front.

Shortly after the half-hour mark, Blues should have doubled their advantage. Quamina was involved again, protecting the ball in an advanced position before finding Sayers, who released Brown with a superb first-time pass. His shot was palmed away by goalkeeper James Dadge, and Anyadike somehow steered the follow-up the wrong side of the right-hand upright.

Although Quamina and Anyadike were later prevented from testing Dadge after receiving the ball inside the penalty area, Coker managed to beat the custodian from Unwin’s pass, only for a defender to clear off the line in the 40th minute. Sixty seconds later, Anyadike sent a dipping shot inches over from 25 yards out.

It looked as though Southend would be going in at half-time with a slender advantage after dominating the opening period, but that lead was wiped out by a fine Cobblers move as Liam Cross twisted and turned on the left-hand side to deliver an inch-perfect cross for Jack Connor to volley home.

“In football, there’s no time to be disappointed, but after dominating for the first 40 minutes and them getting a goal out of nowhere, we didn’t react. In the first minute of the second half we had a great chance and should’ve scored again, but 30 seconds later it was 2-1 to then,” Heath remarked.

The opportunity the coach alluded to fell to Brown after good work by Unwin on the left-hand side. His cross picked out the midfielder, but his shot was directed straight at Dyche on the goal-line. The hosts then went on the attack, with substitute Miguel Ngwa driving the ball in from the right and Cross converting after Andeng Ndi had stopped Connor from netting at the near post.

In the 55th minute, Northampton stretched their lead against a still shell-shocked Blues team. Dyche’s long ball forwards was flicked on by Connor, but Ngwa did the hard work, jinking inside from the right-hand side before firing his shot beyond Andeng Ndi at his near post.

Heath threw on forwards Tayo Adedoja and Kenny Coker, along with defender Luke Reeve, on the hour mark to try and get Blues back into the game, but Northampton almost added a fourth goal in the 62nd minute, with Jaden Crowhurst doing brilliantly to force an attacker to shoot over on the counter-attack.

Midway through the second half, Blues were handed a route back into the game when Anyadike’s effort was adjudged to have struck Dyche’s hand, and the referee pointed to the penalty spot. Unfortunately Oli Coker’s spot-kick was dragged wide and the deficit remained at two goals.

Southend thought they had chalked one of those off on 70 minutes when Brown poked home Oli Coker’s free-kick at the far post, but the assistant referee’s flag was raised for offside, and instead the away team had to be patient.

Blues did continue to probe, but the fluency of the first half was missing and opportunities were largely restricted to set-pieces. With three minutes remaining, after Northampton had failed to clear a right-wing corner, centre-half Tommy Davis marked his 40th youth team appearance with his first-ever goal as he swept home the loose ball to halve the arrears and give Southend hope.

In the final minute of the regulation ninety, a Northampton handball gave Crowhurst the chance to line-up a free-kick from 25 yards out, but his attempt flew over and, during stoppage time, Andeng Ndi had to make a fine save to tip Ngwa’s effort out for a corner at the other end.

Southend threw everything at their hosts in an attempt to preserve their unbeaten record in the Merit League, but their fate was sealed in the fourth minute of additional time when Kai O’Keefe won the ball from Reeve and squared to Tommy Curry, who tucked past the covering Crowhurst on the goal-line.

Blues host Luton Town next Saturday in their final home match of the season, before travelling to Peterborough United to complete the campaign. Heath’s side remain at the top of the league table, although the chasing pack have games in hand at this stage.

Southend United U18s: Collin Andeng Ndi, Harrison Clayden (Tayo Adedoja, 60), Charlie Sayers (Luke Reeve, 60), Jaden Crowhurst, Tommy Davis, Jimmy Wallace, Demaray Anyadike, Cameron Brown (Callum Burkey, 81), Tendi Quamina (Kenny Coker, 60), Oli Coker (Brian Garzon, 81), Bobby Unwin.

Goals: Unwin (21), Davis (87).

Cautioned: Sayers (58, reckless play).