Driving rain battered the Knowsley Road pitch for the majority of the game but Saints held their nerve to record their eighth straight league win this term.
Ade Gardner and Paul Wellens celebrated personal landmarks as the Super League leaders edged past a side they had destroyed 40-16 on the opening weekend of the season.
Gardner opened the scoring with his 50th try in Saints colours before Quins hit back swiftly through Mark McLinden, only for the outstanding Wellens to claim his 100th career touchdown 11 minutes later.
The heavens opened soon after and both sides struggled badly to cope with the slippery conditions.
However, Saints, who won 18-10 at Warrington on a snow-covered pitch last month, ground out victory to consolidate their position at the summit above Leeds.
Daniel Anderson?s side overcame a series of high tackles by the feisty visitors to open the scoring after four minutes.
Lyon failed to convert and Quins, buoyed by the return of skipper McLinden after injury, soon stamped their authority on proceedings.
Quins? half-back pairing of Luke Dorn and Thomas Leuluai dovetailed superbly and their potent partnership led to McLinden barging his way over in the right-hand corner after 13 minutes.
Matt Gafa landed the goal superbly from near the touchline and the visitors, having established a 6-4 advantage, threatened to extend their lead.
The rain began to pour down but the conditions did nothing to quell the visitors? attacking momentum.
Midway through the opening period Tony Clubb almost broke free down the left flank and only a superb last-ditch tackle from Gardner halted the Quins wing.
Two minutes later, though, St Helens hit back with a typically devastating score to regain the lead.
The architect was Sean Long, who collected his own kick and provided an audacious offload to Wellens, who raced over the line from 20 metres.
Wellens celebrated reaching the 100-try mark in his career and Lyon added the extras to edge Saints back ahead at 10-6 at the break.
Harlequins came out strongly after the restart and pinned St Helens back on their own line for long periods.
And tempers began to fray when Talau and McLinden engaged in a brief bout of fisticuffs as tensions threatened to boil over.
But as the rain eventually subsided shortly after the hour mark, Saints sealed the points 10 minutes from time with a close-range try from talented youngster James Graham - and Lyon converted to put the title favourites home and dry at 16-6.
St Helens 16
Tries: Graham, Wellens, Gardner
Goals: Lyon 2
Harlequins RL 6
St Helens: Wellens, Gardner, Lyon, Talau, Meli, Pryce, Long, P. Anderson, Cunningham, Fozzard, Gilmour, Sculthorpe, Hooper. Replacements: Roby, Wilkin, Graham, Fa'asavalu.
Harlequins RL: McLinden, Clubb, Gafa, Smith, Bradley-Qalilawa, Dorn, Leuluai, Tookey, Weisner, Heckenberg, Williams, Hopkins, Mbu. Replacements: Mills, Budworth, McCarthy-Scarsbrook, Sheriffe.
Referee: R Laughton (Barnsley)