Downes had deflected Harry Pell's shot past his own goalkeeper Martin Rice as Neal Ardley's Wimbledon took an 87th-minute lead at sun-drenched Plainmoor.
But Torquay were not to be denied and after piling on the pressure, Downes glanced a deft downward header past diving goalkeeper Ross Worner to convert Kevin Nicholson's cross from the right in the third minute of stoppage time.
Stand-in Torquay goalkeeper Rice made a brilliant reflex save to deny predatory Wimbledon forward Luke Moore in the 42nd minute.
Torquay's on-loan Derby striker Callum Ball came close to breaking the deadlock in the 54th minute with a superb 25-yard strike that beat the diving Worner, but struck the outside of the post.
Rice was Torquay's saviour again in the 62nd minute with a brilliant diving save to palm over Smith's rising shot from the right side of the penalty area.