Match referee Ranjan Madugalle of Sri Lanka also penalised the entire Pakistan team 15 percent of their fees for bowling three overs short in the Rawalpindi game on Tuesday.
Inzamam faces a ban of two to four Tests - or four to eight One-day Internationals - if found guilty of a similar offence over the next 12 months, Madugalle said. "If under Inzamam, Pakistan again fall short by three or more overs in any game for the next year, he could be banned for a specified number of matches," Madugalle said.
Pakistan, bowling second on Tuesday, won the match by 12 runs to level the five-match series 1-1.
This is the second time in as many matches on the current Indian tour that Inzamam has been fined for slow over-rates. Both he and his Indian counterpart Sourav Ganguly were docked 20 percent of their match fees for falling two overs short in the first International at Karachi last Saturday.
That 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.
The Indian team appeared to have learnt from the mistake by sending down the full quota of 50 overs in the available three hours and 35 minutes in Rawalpindi.
Madugalle, however, took no action against Ganguly, who had criticised as "ridiculous" the International Cricket Council's (ICC) rule governing over- rates which imposes only fines instead of the earlier practice of docking overs.
"I find that ridiculous," Ganguly had said at Karachi. "When you are in a tight situation, and when winning and not losing is so important, players don't mind foregoing money."
India and Pakistan play the remaining One-dayers at Peshawar on Friday and at Lahore on March 21 and 24. India will also play three Tests from March 28 on their first full tour of Pakistan since 1989.