The Port Authority's original plan would have doubled for some motorists from $8 to $17 by 2014.
The new plan by Govs. Andrew Cuomo and Chris Christie would raise tolls to $14.50 for some motorists by 2015 comparatively.
Fares on the PATH trains would increase 25 cents a year for four years, instead of $1 next month.
The governors are also ordering a top-down audit of the bi-state agency after a report found the Port Authority of New York and New Jersey paid $86 million in overtime last year.