Mauro Manotas looked to have the winner for the visitors on 90 minutes, but Kendall Waston headed home the Whitecaps' equalizer in second-half stoppage time to give his team a deserved share of the spoils.
An end-to-end opening half-hour saw both teams find chances, but it was Houston that would strike first in 35th minute. Alberth Elis settled a long pass from the Houston backline and picked out Tomas Martinez at the top of the area, who took one touch to his left and slotted an 18-yard shot past Brian Rowe.
The hosts found an equalizer right before half-time when Waston beat his defender with a clever move and cut the ball back to Jose Aja, who hit a first-time volley from a tight angle past Joe Willis to make it 1-1 at the break.
Bernie Ibini-Isei forced a good save from Willis just past the hour-mark, cutting in from the right side and hitting a low curling shot on goal that the 'Caps keeper did well to keep out.
Shortly after, Vancouver's Kei Kamara was shown a yellow card for kicking a Houston defender as he attempted to volley a looping ball out of the air and on goal.
Elis then had a chance for the Dynamo at the other end, getting free in the Vancouver area after some nice build-up play, but shooting right at Rowe, who easily dealt with the effort.
Waston was next in line to try his luck for the Whitecaps and he out-jumped the Houston defense to get his head on a Felipe Martins free kick, but Willis somehow managed to get a hand on the ball to keep the score level.
Aja almost had his second for Vancouver when he beat his defender to the ball at the far post from a set piece but smashed his bullet header into the side netting.
It was one-way traffic for the hosts now and substitute Brek Shea missed an impossibly easy sitter in front of a wide-open net from a Yordy Reyna cross before Waston headed wide narrowly wide of the goal from another Whitecaps set piece.
But just before full-time, a deflected Arturo Alvarez shot fell right to Manotas and he lashed home a lovely volley to beat Rowe right before Waston rose highest to redirect a headed Kamara cross into the net and save a big point for Carl Robinson's team.
Vancouver 2-2 Houston: Waston seals Whitecaps draw - Via MLS
Houston's Mauro Manotas' late goal was offset by Kendall Waston's header at the death for Vancouver, to ensure a late 2-2 draw at BC Place.