Leg-spinner Kumble and seamer Agarkar were omitted from the 15-man touring squad announced on Monday, but were expected to be fit by the time the three-Test series begins on March 28.
The team for the Test matches will be picked on March 22, Board of Control for Cricket in India (BCCI) secretary Karunakaran Nair told reporters after a three-hour meeting of the selection committee here.
Kumble, who suffered a shoulder injury on the recent tour of Australia, is India's most successful one-day bowler with 315 wickets.
Agarkar is recovering from a shin injury, also sustained in Australia.
However, seamer Zaheer Khan and middle-order batsman Mohammad Kaif returned to the squad after missing the one-day series in Australia due to injuries.
Rohan Gavasakar, son of legendary opener Sunil, who toured Australia in place of Kaif, was axed.
With Kumble out of action and off-spinner Harbhajan Singh recuperating from surgery on his bowling hand, India will go to Pakistan without its two leading spinners.
Uncapped Mumbai off-spinner Ramesh Powar was picked after a rich haul in domestic cricket and will share the spin attack with left-armer Murali Kartik.
Zaheer's new ball partners will be Irfan Pathan, Laxmipathy Balaji and Ashish Nehra.
Nehra's selection was subject to his passing a fitness test during a domestic first-class match this week, Nair said.
Captain Sourav Ganguly leads a strong batting line-up that includes one-day cricket's leading run-maker Sachin Tendulkar, the dependable duo of Rahul Dravid and Venkatsai Laxman and the swashbuckling Virender Sehwag and Yuvraj Singh.
Young wicketkeeper Parthiv Patel retained his place in the side despite a mediocre display in Australia.
The Indian cricket board's joint secretary Ratnakar Shetty will be the team's administrative manager, John Wright will be the coach and Amrit Mathur the media officer.
BCCI chief Jagmohan Dalmiya said the team will not be accompanied by a bowling coach, but former world record holder Kapil Dev will assist the selected bowlers during the three-day conditioning camp to be held at the Eden Gardens here from Sunday.
"We want Kapil to monitor bowlers at the domestic level on a regular basis and draw up a training programme for them," Dalmiya said.
The squad will be briefed by security experts at the home ministry in New Delhi on Wednesday morning before departing for Pakistan by a special flight later in the day.
The Indians will play a warm-up match at Lahore on March 11 before the series begins with the first one-dayer in Karachi on March 13.
The remaining games will be played in Rawalpindi (March 16), Peshawar (March 19) and Lahore (March 21 and 24).
The second match in Rawalpindi and the last two games in Lahore will be day-night internationals.
The Test series, India's first in Pakistan since 1989, will be played at Multan (March 28-April 1), Lahore (April 5-9) and Rawalpindi (April 13-17).
India's one-day squad:
Sourav Ganguly (captain), Rahul Dravid (vice captain), Sachin Tendulkar, Virender Sehwag, Venkatsai Laxman, Yuvraj Singh, Mohammad Kaif, Hemang Badani, Parthiv Patel, Zaheer Khan, Irfan Pathan, Laxmipathy Balaji, Murali Kartik, Ramesh Powar, Ashish Nehra (last named subject to fitness).