The England striker headed home a Niko Kranjcar cross on the stroke of half-time, before making the points safe with a goal on the break late on.
Blackburn dominated throughout, with Benni McCarthy twice hitting the woodwork, but it was Spurs who were more clinical with their finishing.
The win sees Harry Redknapp's side move to within a point of second-placed Manchester United, while Rovers are now without a win in six.
The two teams arrived at Ewood Park on the back of contrasting results in midweek. Rovers made six changes to the side that lost 2-1 at Birmingham City, with Lars Jacobsen coming in for the unwell Chris Samba and Michel Salgado making only his second league start, in an unfamiliar right-wing role, in place of the injured Brett Emerton.
Spurs meanwhile named an unchanged side following Wednesday night's impressive 3-0 win over top-four challengers Manchester City.
The hosts made the better start, with the returning McCarthy causing problems early on. On nine minutes, he supplied a brilliant ball in from the right, which Michael Dawson failed to clear, but Franco di Santo could not make a clean connection with his shot.
Five minutes later, Dawson fouled David Hoilett over on the left and McCarthy's inswinging free-kick looped off Aaron Lennon and landed on the top of the bar.
The visitors' first attempt at goal came midway through the half, when Kranjcar played in Jermain Defoe, who fired wide of the far post.
Rovers again threatened, with Hoilett shooting straight at Heurelho Gomes from the edge of the box after a jinking run, before their best chance of the half dropped to di Santo.
After playing a neat one-two with McCarthy, the South African lifted the ball over to his strike partner, whose volley was well kept out by the Spurs keeper.
But despite dominating for much of the opening period, Spurs struck right at the death. One minute came up on the fourth official's board, but 90 seconds into added time, Kranjcar retrieved Tom Huddlestone's sliced shot over on the right and his cross was headed home by the towering Crouch via the woodwork.
Rovers continued to press after the interval and almost equalised eight minutes in. Vince Grella crossed from the right, McCarthy brought the ball down brilliantly on his chest, but his shot, through the legs of Gomes, bounced back off the post and Sebastien Bassong just got in ahead of di Santo to clear.
Further chances came the way of the home team, with di Santo looking to curl one and Steven N'Zonzi then stinging the gloves of Gomes.
Crouch thought he'd added a second when he stooped to head home Lennon's cross on 79 minutes, but he had just strayed offside.
However, the striker did make the points safe seven minutes from time, when substitute Jermaine Jenas flicked a long ball forward into his path and Crouch made no mistake, firing a crisp shot past Paul Robinson.