Otis Khan had given Yeovil a 51st-minute lead from a free-kick before substitute Boco fired home his seventh goal of the season in added time to ensure Stanley netted for the first time in seven-and-a-half hours of play.
It was an even first half with limited chances at either end.
Yeovil frontman Khan beat the offside trap on 15 minutes but his shot was kept out by the sliding legs of a Stanley defender.
Stanley's best effort was a 20-yard curling shot by John O'Sullivan which just went over on the half hour.
The game was stopped in the 38th minute when Stanley's on-loan Bristol City defender Zak Vyner fell to the ground breathing heavily and was stretchered off to receive further treatment.
Unmarked Mark Hughes headed over for Stanley just before the break while Tom Eaves came close for Yeovil but was denied by the legs of Elliot Parish.
The visitors opened the scoring six minutes after the interval when Khan's free-kick from 20 yards, following a Paddy Lacey foul, sailed through a sea of bodies and nestled in the bottom corner.
Ryan Hedges came close to adding a second minutes later but his shot was across goal and just wide.
Stanley pressed without testing Artur Krysiak while Eaves fired narrowly over the bar for Yeovil.
Then, with four minutes of added time on the board, Boco got the ball from Gary Taylor-Fletcher and fired home a much-needed equaliser.