After bad weather had put paid to Friday's opening day, the Warwickshire skipper made 115, the left-hander's innings featuring four sixes and eight fours as the visitors declared on 345 for five.
Bad light cut short the day's play before MCC could begin their reply.
"I was a bit scratchy at first, but we haven't played any competitive cricket until today," said Knight.
Knight, who won the toss Friday before rain and snow put paid to any hopes of play, shared a 130-run opening stand with Mark Wagh.
Waugh, just beaten to his half-century by Knight, fell for a 66 featuring 14 boundaries when he chipped Nottinghamshire off-spinner Graeme Swann to David Harrison at deep mid-off 15 minutes after the lunch break.
Knight almost went the same way, when on 70 he chipped Swann to Harrison, now at deep mid-on, only for the regulation catch to be dropped.
The former Essex batsman, who retired from international cricket after the 2003 World Cup in South Africa, cashed in with a straight six off Swann.
At the other end Ian Bell was looking for runs to help him force his way into the England side ahead of next month's first Test against Bangladesh at Lord's.
But he fell for 14 after pulling Glamorgan pace bowler Harrison to deep mid-wicket.
Knight eventually went eight overs later when a reverse sweep off Swann was caught by Mike Pettini at backward point.
South Africa-born Jonathan Trott smashed a rapid 75 off 98 balls before he was caught off Harrison who finished with three for 70.