Match referee Ranjan Madugalle docked the two skippers 20 percent of their match fees and the rest of the players 10 percent each after both teams fell two overs short during Saturday's high-scoring thriller in Karachi.
The match ended as the highest scoring One-dayer in history after Pakistan, replying to India's mammoth 349 for seven from 50 overs, fought back superbly to reach 344 for eight.
Ganguly criticised as "ridiculous" the International Cricket Council's (ICC) rule governing slow over rates which imposes only fines for slow over-rates instead of the earlier practice of docking overs.
"It's of no help to the side fielding second," Ganguly said. "The old rule was okay where a team with a slow over rate in the first innings was docked overs when it batted."
Pakistan's bowlers, who conceded five extra overs by sending down 30 runs in wides and no-balls, took almost 20 additional minutes to complete their 50 overs.
But the outspoken Indian captain was not amused to learn later that Pakistan's batsmen still had 50 overs available to them.
"At the break, when I went to the match referee to ask how many overs Pakistan had to get the target in, he said there would be no overs docked," Ganguly said.
"I find that ridiculous. When you are in a tight situation, and when winning and not losing is so important, players don't mind foregoing money."
Ganguly had been similarly hauled up on the recent tour of Australia for slow over-rates during a Test match.
India and Pakistan play the second of five One-dayers in Rawalpindi on Tuesday.
India will also play three Tests from March 28 on their first full tour of Pakistan since 1989.