The toll closed at 6.30 Tuesday evening and comes into force again at 6.30 Wednesday morning.
The first day was hailed a success by officials, who warned that the real test would come next week when most Swedes return to work and school after the festive break.
Morning rush hour was down by 16 percent from Monday.
A city-wide referendum on September 17 will determine whether or not the charge should be made permanent, with two out of three Stockholmers opposed to the tax, according to a recent poll.
There were some protests on Tuesday. One person tried to destroy a computer unit in one of the pay stations, by setting fire to it.
In addition, a transponder, the device used for instant payment through a driver’s bank account, was also stolen.