The players were cited by on-field umpires Billy Bowden and Aleem Dar as well as TV umpire Suresh Shastri after they clashed on the opening day of the match at the Feroz Shah Kotla stadium here.
Gambhir appeared to elbow Watson after the all-rounder seemed to mutter something to the Indian batsman as he took a second run in the 51st over of Wednesday's play.
The opener was charged with a level two offence for conduct contrary to the spirit of the game, an International Cricket Council (ICC) statement said. Watson was charged under the same clause but with a less serious level one offence.
The hearing before match referee Chris Broad will take place after the second day's play.
Gambhir, Watson come close to face off
Gambhir runs the risk of a fine or a suspension from either one Test match or two one-day internationals while Watson faces an official reprimand or a fine.
The Indian opener was fined 65 percent of his match fee during the Kanpur Test against Pakistan in November 2007 for a run-in with Shahid Afridi.
India's left-arm paceman Zaheer Khan was docked 80 per cent of his match fee for his verbal send-off to Matthew Hayden during the second Test in Mohali, which India won to go 1-0 up in the Border-Gavaskar series.