The umpire erred in his last Test series before retiring out of the ICC's elite panel prompting India to complain.
Harper decides to walk after being stumped by India's objection
Harper pulled out of the third Test in Dominica from July 6. He had been due to retire from the International Cricket Council's elite panel of umpires after the match.
"The real shame is it deprives him of the opportunity to sign off as a Test match umpire in a befitting manner," the ICC said in a statement.
Harper will be replaced by Richard Kettleborough.
India's players were said to be unhappy with some of Harper's decisions in the first Test at Kingston. The visitors lead 1-0 with the second Test currently being played in Barbados.
"The reality of the situation is that Daryl's statistics show his correct decision percentage in Tests involving India is 96 per cent, which is considerably higher than the international average for top-level umpires," ICC general manager of cricket David Richardson said in the statement.
The 59-year-old Harper officiated in 95 Tests, 174 one-day internationals and 10 Twenty20 games.
He made his international debut in 1994 in a ODI between New Zealand and South Africa at the WACA in Perth. He officiated in his first Test during the 1998 Ashes series at the same venue.