The injury also kept express bowler Bond out of the first Test at Centurion, which South Africa won by 128 runs.
New Zealand manager Lindsay Crocker said the decision to send Bond home was made after he failed a fitness Test in Cape Town yesterday.
''He bowled for six overs yesterday, and just as he was cooling down it became obvious to him that his knee clearly wasn't right,'' Crocker told Reuters from Cape Town today.
''He looked like he got through it okay, but then it started to hurt. He knew himself that it wouldn't be right for this match or the next one.
''We came to a mutual agreement that he's better off going home and getting it properly right.'' Bond, who has taken 64 wickets in 14 Tests, is one of the fastest bowlers in the game but also one of the more injury prone.
Bond made his comeback to the Test arena in Zimbabwe earlier this season after spending two years on the sidelines because of stress fractures.
New Zealand summoned Michael Mason as cover for Bond during the first Test, but Crocker said Mason's inclusion in the team to play the second Test was not assured.
''He's in the mix, just like every other fit member of the squad,'' Crocker said.
The second Test starts in Cape Town on Thursday.