The drop is in contrast to estimates that Thanksgiving and Black Friday sales at brick-and-mortar stores rose 2.3%.
The average consumer spent $407.02 over the whole weekend, down 3.9% from last year.
The number of shoppers increased to 141M people from 139M.
The fall in spending came after retailers warned of a difficult holiday season and was due to the aggressive bargains on offer, a trend that is expected to continue.
However, the NRF maintained its forecast that retail sales will grow 3.9% for the whole holiday whole season.
Online sales climbed 17.3% on Thanksgiving and Black Friday, ComScore estimates, noting that the latter day attracted a record $1.2B in spending. The research firm expects Internet sales to rise 16% for the whole of the holiday season.
Total e-commerce sales hit $20.6B in the first 29 days of this holiday season, up 3.1% from last year, although this year includes more days.
Today is Cyber Monday, which the NRF reckons will attract 131M shoppers vs 129M last year. But as with Black Friday, Cyber Monday has started a day early, with J.C. Penney (JCP) and Macy's (M) among those who began related promotions yesterday. Target has gone further and created "Cyber Week."
More on Thanksgiving sales.