Side had keeper Ryan Karrer to thank early on. The veteran keeper saved a penalty from Clapton's Jacob Kromann, which was won George Woodward was adjudged to have handled in the area, in the opening minute if the match.
Kromann was denied again by Karrer on ten minutes, with the keeper stopping a header from the Danish forward from Ryan Reed's accurate corner.
'Side had chances of their own to score but Max Bolton twice was denied by Clapton goalie Emmanuel Olajide, before Isaac Marfo failed to make the most of an opportunity after being picked out by Joe Thomas.
After a goalless first-period both teams came out with attacking intent after the break. Max Bolton fired a shot over for 'Side before Kromann saw a shot deflected wide. Clapton then saw a further chance missed when Jaydon Charles broke through, only to see his one-on-one effort saved by Karrer.
Alex Goldstone's Sky Blues took the lead on 70 minutes from the penalty-spot. Seconds after Thomas saw a shot strike a hand in the box, Dan Jones was brought down in the area. The experienced midfielder kept his cool to fire the spot-kick home, with the ball just creeping in past Olajide in goal.
Sadly Giovanni Palmer equalised for Clapton just a minute later, as 'Side's lead was a short one. Kromann picked out the forward who fired in a low awkward shot into the far corner to equalise,
Charles then fired over for Jon Fowell's men before 'Side substitute Craig Jeakins was denied by Olajide who smartly tipped a shot wide, to deny 'Side grabbing the three points.
Deep into three minutes of injury-time, Clapton grabbed the latest of winners. Andy Greenslade reacting fastest, finishing well after a scramble in the area from a long throw-in. It was harsh on 'Side, who deserved to take something from the game for their efforts.
The result saw 'Side slip back to 20th and bottom of the table, following Leyton Athletic's draw with Enfield 1893 lifting them up into 19th. That leaves 'Side now seven points from safety from 18th placed Southend Manor.
'Side are next in action on Saturday 2nd March when we face Ilford at Cricklefields. The Sky Blues are the 'away' team in this fixture, which will kick-off at 3pm.
'Side: Ryan Karrer, Frederico Hernandez (Connor Goldstone), George Woodward, Joe Thomas, Harry Matthews, Edward Lang, Joe Oates, David Ottley, Isaac Marfo (David Hornsby), Max Bolton (Craig Jeakins), Dan Jones