Neither side could break the deadlock in last week's first leg at Sincil Bank, but the Grecians opened the scoring on the night and in the tie just before the half-hour mark.
The visitors managed to get the ball into the back of the net on 40 minutes through Elliot Whitehouse, but referee Darren England ruled the goal out due to an apparent Matt Rhead handball in the build-up.
Exeter then doubled their lead in spectacular fashion shortly after the restart, Hiram Boateng surging from inside his own half and past three challenges before curling home from the edge of the box.
Ryan Harley added another sublime goal for the hosts on 69 minutes, connecting with a half-cleared corner on the edge of the area to rifle a half-volley into the roof of Ryan Allsop's net and all but kill off the tie.
Although Matt Green pulled a goal back 12 minutes from time, Rhead setting up his teammate to poke beyond the onrushing Christy Pym, the result was never in doubt and the final whistle saw Exeter celebrate a second consecutive playoff final appearance.
The Devon side will take on either Notts County or Coventry City at Wembley Stadium on Monday, May 28.
EXETER CITY (4-4-2): Pym; Sweeney, Storey, Moore-Taylor, Moxey; Taylor, Boateng (Archibald-Henville 76'), Tillson, Harley; Simpson (James 85'), Stockley
LINCOLN CITY (4-3-3): Allsop; Wilson, Waterfall, Bostwick, Eardley; Woodyard, Frecklington (Pett 73'), Whitehouse; Green, Anderson (Palmer 55'), Rhead