It had seemed likely that a 13th-minute strike by Gary Birch would separate the sides as Northampton rarely looked like penetrating the visitors' defence.
But all that changed in the third minute of added time when a hopeful ball over the top caught the City defence napping and Low latched on to it and lobbed visiting goalkeeper Alan Marriott
It meant the sides repeated the 1-1 draw they played out on the opening day of the season, when Lincoln's top scorer Birch had also been on target.
On this occasion he hooked in a volley after showing neat control in bringing down a right-wing cross from former Northampton striker Derek Asamoah.
Asamoah, whose last visit to his old stamping ground saw him sent off for Mansfield, had a much more productive afternoon and a fifth-minute run teed up Birch, who squandered a good chance.
Gareth McAuley then headed across goal from a Dean Keates free-kick as the visitors called the early shots.
Northampton's best first-half effort arrived when Andy Kirk forced a diving save from Marriott, who also had to hold a drive from Martin Smith.
Lincoln could have added to their tally immediately after the restart when Asamoah pulled a ball back from the byline for Nat Brown, whose rising drive was pushed over the crossbar by Lee Harper.
Then Brown again went close with a diving header from Paul Mayo's free-kick before Jason Crowe blazed wide at the other end.
Northampton's frustrations became increasingly apparent as four of their players were shown yellow cards by referee Andy D'Uso.
Despite one delightful three-man move involving Scott McGleish, Ian Taylor and Junior Mendes, which ended with a shot by the latter well saved by Marriott, the Cobblers were heading for defeat until Lincoln's fatal late lapse.