Adam Bogdan's howler saw Ed Upson score for the visitors with just over 10 minutes left, and another defeat would have added to Bolton's miserable start to the season.
But Matt Mills' header in injury-time rattled against the post and Baptiste nodded in the rebound to give the Trotters a point which sees them move off the foot of the table.
All three new loan signings made by Bolton boss Dougie Freedman this week did not make the starting 11. Both Liam Feeney and Neil Danns, from Millwall and Leicester respectively, were named among the substitutes, whilst Cardiff's Kevin McNaughton missed out completely.
Yeovil manager Gary Johnson handed a debut to young defender Shane Duffy, who is on a month's loan from Everton.
Medo Kamara had the first real chance to open the scoring early on. His drilled shot from 25 yards rattled the inside of the post to the relief of Yeovil goalkeeper Wayne Hennessey.
The visitors then almost broke the deadlock five minutes before the break. Andy Williams slid a ball through to Paddy Madden, who forced a smart diving save from Hungary international Bogdan.
In the final minute of the half, Wanderers had the best opportunity to go in ahead. A loose ball fell to Lee Chung-Yong, who seemed to have too much time to think about his shot before forcing Hennessey to parry the ball out with his chest.
The Trotters then came out in the second half looking to make amends for their flat performance. A breakaway move saw Lee and Chris Eagles play a one-two before the South Korea international fed in David Ngog, but the Frenchman failed to curl his shot into the net.
Feeney then came on alongside Jermaine Beckford, with the latter almost making a massive impact.
Kamara cut the Yeovil defence wide open with his through-ball sending Beckford one-on-one with Hennessey. The Wales international goalkeeper came out on top, catching Beckford's effort to the frustration of the home fans.
Eagles then put Beckford clear on the counter once more, with the former Everton forward's first-time shot curled wide.
Just as the home outfit were starting to look like the more likely to score, the moment of madness happened.
A speculative effort from over 30 yards by Upson looked to have dribbled its way into the hands of Bogdan. But instead, the ball agonisingly slipped through his legs and crawled over the line.
Baptiste's late header then saw Bolton level, with Zat Knight almost snatching all three points for the hosts with a header of his own in the last second.