The Argentinian striker was rested for Saturday's 2-0 loss at Hull in which Leeds failed to register a shot on target, but he showed his team-mates how it was done as he scored his 18th goal of the season from the spot after 65 minutes.
Bolton could stake a claim for an undeserved defeat - they had the best of a torrid first half during which they hit the post - but in the end Leeds just about edged it owing to their second-half improvements.
Becchio's goal after Tyrone Mears' clumsy foul not only earned Neil Warnock's men a fifth straight home win for the first time since 2009, it also booked him a spot in Leeds' all-time top-10 leading goalscorers on 76.
With Rodolph Austin's deflected 12th-minute free-kick skipping wide Leeds had already improved on their dismal display at Hull on Saturday where they did not register a shot, and even though the Jamaica midfielder was also off target with the next effort, they were at least showing some attacking intent.
In spite of their chances, Leeds were well off the pace in the middle of the park and should have been behind in the 20th minute.
Darren Pratley robbed Alan Tate of possession in the centre circle and he and Kevin Davies worked the ball to a clean-through Chris Eagles, but his shot clipped the post and went behind.
After more good work from Pratley, Eagles should have done better from the edge of the box, before the tricky winger brought about the best moment of an awful half when he forced Paddy Kenny to tip his 35-yard shot around the post.
In the second half Leeds built an attack with Austin going down the right and, after his cross was not cleared, David Norris' mishit pass rolled into McCormack who was ungainly bundled over by Mears, allowing Becchio to send Adam Bogdan the wrong way for the second time this season.
All of a sudden there was some energy inside Elland Road and El-Hadji Diouf sent McCormack clear but he rushed his shot and found the stand, before Becchio headed a Diouf corner over.
Bolton had to raise their own game and David N'gog shouted in vain for a penalty when he was tackled by Tate, but they had no way of getting a clear sight of Kenny's goal and were left to rue Eagles' first-half near miss.