A debut home goal by on-loan striker Renei Batlokwa secured Lowestoft a crucial three points in their battle to avoid relegation.
Harvey Hodd had put Lowestoft in front in the first half, before Hendon equalised through Zak Joseph.
But it was Batlowka's low drive on 70 minutes that proved the difference for Dale Brooks' side.
Lowestoft, playing their first of four games in the space of seven days, created the first chance as Jacek Zielonka shot straight at keeper Lovelock.
Play-off contenders Hendon then forced keeper Elvijs Putnins into a save as Zak Joseph tried his luck. The visitors went even closer on 18 minutes as the league's leading scorer Niko Muir saw his header cleared off the line by Adam Smith.
It was clear Lowestoft would have to defend with their lives to get anything from the game, but they were willing to put their bodies on the line to prevent Hendon taking the lead.
But surprisingly, against the run of play, it was the Trawlerboys who seized the initiative in first-half stoppage time. Robert Eagle's shot from the edge of the box was spilt by Lovelock and Hodd was on hand to side-foot home the rebound to give Lowestoft a crucial lead.
After the break, Lowestoft made the worst possible start, conceding on 51 minutes. Joseph's sweet strike from 25 yards, his 17th goal of the season, gave Putnins no chance and brought the scores level.
Home keeper Putnins had to be alert to save from Rian Bray and Joseph as the away side upped the pressure.
But remarkably, Lowestoft showed real character to take the lead for the second time on 70 minutes, virtually out of nothing as Southend United loanee Batlokwa drilled a shot past Lovelock from the edge of the box.
Lowestoft got the slice of fortune they needed in stoppage time as substitute Casey Maclaren headed over from six yards – meaning the Blues claimed their first win in nine matches.
Lowestoft: Putnins, Zielonka, Humphrey, Fisk, Cole, McAuley, Hodd (Schaar 72), Smith, Bammant (Machaya 90), Batlokwa, Eagle.
Subs not used: Wren, Leslie.
Ref: Ryan Head. Att: 305
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