The Iron made one change from the team that faced Oldham Athletic in midweek, as Beestin came in for Lewis Spence.
An early right-wing corner from Alex Gilliead saw Kevin van Veen try to force an effort towards goal at the near post but it was blocked away.
Soon after, in the fifth minute, Gilliead was able to sidestep Alan McCormack and get into the box. His cross took a deflection and was sent out of the area to Jem Karacan, who saw his shot deflected, with Mark Oxley gathering.
With 10 minutes gone, McCormack attempted to stall the taking of an Iron free-kick by tying his laces in front of the dead ball. Nevertheless, the Iron played it short to van Veen, who saw a curling, looping shot go just over the bar.
Six minutes later, superb link-up play between Loft and van Veen saw the former lift over the head of John White for the latter. Van Veen then curled a 30-yard effort just over the bar.
On 17 minutes, Southend's Reeco Hackett-Fairchild controlled well on the left before cutting inside and firing a right-footed effort over the bar.
Two minutes after that, Simeon Akinola hooked the ball across goal towards Ricky Holmes but he couldn't get a clean connection on the strike as it ran through to Mark Howard.
Van Veen and Loft looked to link up again with 26 minutes played following a good pass from Beestin, but Loft couldn't quite reach the return. Gilliead strode forward and did win a corner though.
From it, van Veen's delivery was met by a far post header from Loft, with the ball going just wide of Oxley's right-hand post.
Soon after, the Iron won a free-kick 30 yards from goal after Gilliead had fed the ball into Loft, but nobody could connect with van Veen's subsequent ball into the danger area.
Akinola took down a ball over the top in the 37th minute and nudged the ball past Howard, with Clarke there to calmly control and clear.
Southend's Timothee Dieng was teed up the ball on the edge of the area in the 44th minute, but his shot bobbled across goal and wide of Howard’s left-hand post.
The final and third minute of first half stoppage time saw a chance for Southend as the ball came low into the box from the left, but the shot was fired just wide by Holmes.
Early in the second period, Beestin won a free-kick down the left channel for the Iron after being fouled by Holmes. Van Veen went short to Green, who hung in a cross, with the ball headed away.
A second cross was then put in from the left, with Jacob Bedeau ending up on the ground as the ball came towards him. A goal kick was given.
After 58 minutes, McCormack hit a half-volley towards goal from 25 yards which required Howard to palm the ball over the bar for a Southend corner.
The first Scunthorpe change was made in the 64th minute when Abo Eisa came on for Loft.
A minute later, Kyle Taylor was teed up on the edge of the area, but he lashed his 20-yard effort over the bar.
With 70 minutes played, after going down on the edge of the penalty area in need of treatment, van Veen was replaced and John McAtee came on.
Scunthorpe hit the post in the 72nd minute when Eisa opened up 25-yards from goal and had a go, with his low effort beating Oxley, but coming back into play off the upright.
Southend were handed a penalty on the 79th minute when Clarke committed a foul in the penalty area, for which he was sent off, and Ashley Nathaniel-George stepped up to score past Howard.
A double United change was made in the 88th minute as Rowe and Green were replaced by Teddy Howe and Myles Hippolyte.
Just moments later, the Iron were level as Karacan got the ball down on the edge of the area, and Beestin moved the ball onto his left foot before slotting beyond Oxley for his fourth goal of the season.
There were eight minutes of added time but no further chances as the game ended all square.
United return to action on Tuesday night when they host Bradford City at the Sands Venue Stadium (7pm kick-off).
IRON: Howard, Clarke, Bedeau, Gilliead, Loft (Eisa, 64), van Veen (McAtee, 70), Brown, Green (Hippolyte, 88), Beestin, Karacan, Rowe (Howe, 88).
IRON SUBS NOT USED: Watson, Spence, O'Malley.
SOUTHEND: Oxley, McCormack (Taylor, 61), Hobson, Dieng, Akinola (Goodship, 70), Hackett-Fairchild (Mellis, 82), Demetriou, Hart, Ferguson, White, Holmes (Nathaniel-George, 61).
SOUTHEND SUBS NOT USED: Seaden, Cordner, Acquah.