Ten-man Chester put in a spirited late effort but were edged out at the Jakemans Community Stadium.
Just five minutes after Declan Weeks had missed a Blues penalty, Liam Edwards was sent off and Martin Woods converted from the spot kick at the other end in what was the only goal of the game.
Calum McIntyre made two changes from last Saturday’s FA Cup triumph, as Matty Williams and Kevin Roberts replaced Harrison Burke and George Glendon – who both dropped to the bench.
It took 16 minutes for the first opportunity of the game and it fell to the hosts, as Brad Nicholson nodded Martin Woods’ corner just wide.
Chester almost had a clear opening on the counter when Iwan Murray released Charlie Caton moments later, but Nicholson made a crucial last ditch sliding challenge.
Then the Blues had a goal disallowed as Cameron Gregory made a mess of a deflected cross and allowed Murray to score, but Referee Jack Hall decided the ‘keeper had been fouled and awarded a free kick.
A real blow would follow for the Blues as Caton limped off due to injury on 37 minutes, loanee Connor Evans was his replacement.
Wyll Stanway would then ensure the scores were level at the break, out quickly to thwart Kelsey Mooney who was played through on goal in the final minute of stoppage time.
The Seals had the chance to take the lead early in the second half, as Murray fed Evans who was tripped inside the box by Tyler Knowles.
Up stepped Declan Weeks but the Captain was denied by the diving Gregory who tipped it behind.
Chester were having a promising spell though and continued to press, as Joel Taylor’s cross was headed inches wide by Adam Thomas.
However, the game was about to change moments later. Liam Edwards was then adjudged to have fouled Keaton Ward inside the box, and was sent off for a second bookable offence.
Up stepped Woods who fired the penalty confidently beyond Stanway to open the scoring.
The ten-men though weren’t to be deterred in their efforts for a point and started to create extended spells of possession and pressure. However, countless crosses from Sparrow on the right and Taylor on the left just failed to find their targets.
Club Captain George Glendon came on for his 100th Chester appearance, and nearly set up an equalising moment as Whitehouse released him on the left – but his low cross was well cut out by Bostwick.
At the other end Boston had opportunities on the counter, but Stanway stood up well to save from Keaton Ward and Knowles.
Weeks had a shot deflected over late on and as the Blues pressed the Pilgrims scored but the flag was up for offside, meaning it finished 1-0.
Chester: Stanway, Sparrow, Williams, Edwards, Taylor, Roberts, Weeks, Murray (Glendon 73), Whitehouse, Caton (Evans 37), Thomas (Burke 60).
Subs Not Used: Coates, Maguire.
Scorers: Woods (pen) 56.
Attendance: 1,610 (111 Chester).