Greg Tempest came close at the other end moments later, and it was the visitors who eventually broke the deadlock with just seven minutes remaining until half time.
Tom Richards looked to provide an instant response for the Shots, who picked up an FA Cup draw with League One side Bradford on Sunday, but he couldn't keep his effort down as his side went in one behind.
The Imps were the first to threaten in the second half as Phil Smith somehow managed to prevent Wootton from doubling his tally, and that save proved doubly important when the hosts levelled things up 20 minutes after the interval.
Again it came from a corner, with Lincoln unable to clear their lines before the ball was fed back into the area for 18-year-old Stevenage loanee Dipo Akinyemi to flick home on his debut for the club.
Smith denied Wootton again 10 minutes later, but Lincoln would eventually restore their advantage in the 80th minute as Jack Muldoon's 25-yard strike left the keeper wrong-footed on its way in.
That proved to be the winner as Aldershot saw their six-game unbeaten streak come to an end, while Lincoln themselves snapped a two-match losing run.