Bengal were 11 overs in arrears, including seven in the first innings, something that has happened for the second time this season after Saurashtra match.
Shukla's teammates were fined 50 percent of their match-fees for the same offence.
"As it has happened for the second time, it's termed as 'serious offence' and hence the captain is docked the full match fee," Match Referee Rajendra Jadeja told reporters.
In fact, Shukla has to ensure that the team bowls within the permissible limit in their semifinal against Maharashtra to avoid a ban in case Bengal make the final.
Bengal face Maharshtra in the Ranji last four in Indore from January 18-22.