LINNETS climbed into the play-off positions for the first time this season as Ryan Brooke headed off a Bootle fightback.
Brooke struck at the double to go joint sixth in the club's all-time scoring charts, after the hosts had suddenly threatened to derail a dominant Runcorn display.
The away team made it harder than it should have been by not making the most of their many chances before the break.
However, Bootle's new 'keeper Ryan Bopda took a lot of credit for holding the visitors at bay until the 44th minute.
There was a blip for Runcorn upon the restart, Bootle pulling level just before the hour.
But the visitors reacted well to reassume command.
They achieved a second successive victory for the first time since the opening week of the Pitching In Northern Premier League West campaign.
Linnets' stay in fifth place will hinge on results from the main body of fixtures tomorrow but prospects are looking brighter for the Yellow & Greens.
Manager Billy Paynter made one change from the XI, which started last Saturday's 2-0 home victory over Vauxhall Motors.
Kenny Brown was recalled after being discharged (if only temporarily) from the injured list, Joe Lynch stepping down.
James Hooper began his second spell as a Runcorn player alongside Lynch on the substitutes bench, although both would join the fray in the second half.
Brown, meanwhile, lasted only 34 minutes before succumbing to a pulled hamstring.
Friday night football had drawn a crowd approaching 750 to Berry Street Garage Stadium and before kick-off, they observed a respectful minute's silence.
This was in tribute to Everton chairman Bill Kenwright and England and Manchester United legend Sir Bobby Charlton, who had passed away earlier in the week.
Quicker out of the blocks, Runcorn went close to a 12th-minute lead.
James Short's cross was deflected towards his own goal by Bootle defender James Cooper, whose blushes were spared by Bopda's quick reactions when turning the ball around the post for a corner.
Runcorn had started brightly and positively, Olly Molloy and Lewis Doyle also bringing Bopda into early action.
Bootle responded by forcing their first corner in the 21st minute from which there were loud penalty appeals for handball. But referee Kavan Hurn was having none of it.
Runcorn soon reverted to attack and Bopda, by far the busier 'keeper, again had to show his credentials to deal with a curling Doyle shot.
Adam Moseley, on for the stricken Brown, soon got involved as Linnets continued to probe but the teenager couldn't keep down his left-foot shot from a promising position.
A 40th-minute attempt by Brooke was then blocked for a corner before Bootle had their first genuine sight of the Runcorn goal, Owen Robinson driving wide.
Bopda had been the biggest influence on the first half remaining goalless for so long and Molloy was next to be denied by the debut-making Bootle No.1.
However, Bopda was finally beaten with stoppage time fast approaching.
The 'keeper again did well to save from Sam Barratt, but couldn't prevent the handily-placed Brooke from snapping up the rebound.
The breakthrough had been coming, the away side no doubt feeling at half-time that their lead could and should have been greater.
This might have caused unease, which only increased upon the restart. Bayleigh Passant had to make his first serious contribution of the evening with a fine save.
Bopda kept Bootle in contention by turning away a Will Saxon effort before Molloy set up Moseley for another strike on goal, which was blocked by Arthur Lomax.
It was Molloy's last involvement, the former Charnock Richard centre forward making way for Hooper, getting his first Runcorn appearance second time around.
Bopda's earlier heroics were richly rewarded in the 59th minute, when Jake Burton's curving shot beat Passant.
The momentum change was clear for all to see, Sam Burns promptly being thwarted by the Linnets 'keeper.
Runcorn were obviously disconcerted by a switch in formation which followed their two substitutions - a solid-looking 4-4-2 being succeeded by an unsettled 4-2-3-1.
It seemed that attack was now the best form of defence as Saxon's cross to the far post was cleared off the Bootle goal line.
From being in control of the game, Linnets were suddenly looking anything but - until the returning Hooper made a timely intervention.
Cutting inside onto his left foot, the English import from Australia delivered a superb cross, which was converted at point-blank range by Moseley in the 71st minute.
Lynch replaced Doyle in a like-for-like central midfield swap and with 11 minutes left to play, Ryan Brooke took Runcorn further away from their Merseyside hosts.
Saxon was brought down by Lewis Earl in trying to seize on Brooke's through ball.
Brooke was a picture of concentration as he confidently dispatched the resulting penalty straight down the middle. His sixth goal of the season was the 60th of his Linnets career.
Bootle weren't showing the white flag and in the closing minutes, it needed an excellent Sam Barratt clearance to retain Runcorn's two-goal advantage.
But ultimately, nobody could argue with the result which will lift Runcorn's spirits after a difficult start to their season.
Runcorn Linnets: Bayleigh Passant, Sam Barratt, James Short, Jacques Welsh, Peter Wylie, Antony Kay, Will Saxon, Lewis Doyle (Joe Lynch, 75 mins), Oliver Molloy (James Hooper, 55 mins), Ryan Brooke, Kenny Brown (Adam Moseley, 34 mins). Subs (not used): Eden Gumbs, Josh Roberts (GK).
Photo: Ryan Brooke celebrates his second goal with James Hooper. (Picture by Tom Paul).