Batting at number nine, the Australian reached his hundred off only 72 balls, hitting three sixes and 15 fours, as his county ammassed 328.
Warne's previous best score was 99 against New Zealand in 2001.
Another Australian Simon Katich made 56 but Kevin Pietersen, keen to impress before the England squad is named this weekend, managed just one. Kent closed on 135 for three with David Fulton 64 not out.
England opener Andrew Strauss' miserable start to the season also continued as hit hit just 27 in Middlesex's 390 against Gloucestershire at Lord's.
But Ed Joyce (75), Paul Weekes (69), Owais Shah (63) and Ben Scott (58) all made half-centuries as the home side scored heavily on the first day.
Yet wickets fell regularly with Steve Kirby - currently at the centre of ball-tampering allegations - taking three for 84 and Jon Lewis four for 82.
Gloucestershire were nought without loss after one over of their response.
The other team embroiled in ball-tampering controversy this week, Surrey, made the most of their opportunity to bat against Glamorgan as they piled up 441 for seven at The Oval.
Scott Newman (117) and Rikki Clarke (85) steadied the innings after two early wickets with a stand of 185 before Ali Brown did what he does best.
Brown smashed 122 in 116 balls with 21 fours and two sixes and James Benning also weighed in with a run-a-ball 57.
Sussex took the upper hand on the second day at Hove, adding an extra 130 to reach 412 in their first innings before reducing champions Warwickshire to 141 for five in reply.
Nick Knight and Mike Powell (both 45) got Warwickshire off to a solid start but two wickets each from Jason Lewry and Mushtaq Ahmed changed the complexion of the innings.