The Scottish League Two club were late with a £3,320.20 tax payment.
They then fielded a player, Ross Millen, who had been registered after their "event of default", which should have prompted a registration embargo.
But the club's ban on registering players and playing those registered after 16 January has been lifted.
The SPFL says the club "gained no sporting advantage", was unaware of the event of default relating to the missed tax payment until after the 2-0 loss to East Fife, in which Millen played, and since then neither of the two players registered after 16 January - including Millen - have played for the club.
Clyde had stated there are now "fully up to date with all HMRC liabilities".
Manager Barry Ferguson brought in four new players during the January transfer window and the club could have been banned from fielding those players.
However, the SPFL said in a statement: "Clyde FC admitted all alleged breaches of SPFL rules.
"The SPFL board sub-committee found that all breaches were inadvertent and had arisen as a result of extraordinary circumstances affecting the club and one of its directors at the relevant time.
"Clyde FC were censured, warned as to their future conduct and given a £2,500 fine suspended until the end of season 2016-17 (to be activated in the event of future breaches of SPFL rules in this area).
"At an SPFL board meeting following the sub-committee hearing, the ban on Clyde FC registering any new players and on playing those players registered after 16 January 2016 was lifted with immediate effect.
"Clyde FC was reminded of its rights of appeal in terms of the Scottish FA Judicial Panel Protocol."
And Clyde said on their website: "The club can confirm that it is satisfied with the ruling and has no intention of pursuing the option of an appeal."
Clyde have been censured and given a suspended £2,500 fine after the club admitted breaches of Scottish Professional Football League rules.