The punishments relate to Darren Morris' involvement in Leicester's Zurich Premiership clash with London Irish on September 13 and that of James Parkes for Saracens the following day at Newcastle.
A statement from the Board of England Rugby said: "The Board took into account the circumstances surrounding both incidents and the statements of mitigation from both clubs.
"The Board decided that Leicester Tigers should be sanctioned with the loss of one point and Saracens with the loss of two points.
"The Board also stated that the playing of unregistered players will always result in a points deduction and in this year's regulations there is no maximum figure."
Leicester boss Dean Richards was disappointed with the decision, but stated that the club will not be contesting the penalty.
"The registration procedure is a straight-forward procedure," he said.
"We did, however, omit to include a release paper, but did ask to be informed if any further documentation was required.
"The registration papers were submitted to the RFU nine days before the registration deadline and we received a verbal notification that all of our players were registered to play. We were not alerted to the fact that there was a problem for a further 17 days.
"Although we have accepted that we have made an administrative slip-up, the facts show that the Rugby Football Union was equally to blame.
"We also disagree with the decision of England Rugby to name the player concerned. This is an administrative error and not a playing issue and to bring that player's name into the public domain is completely unnecessary."
The deduction means that Saracens are reduced to four points and drop to second from bottom at the foot of the Zurich Premiership, just above Rotherham.
The club have said that they would review the reasoning behind the loss of points for what they consider to be an unintentional breach of the regulations and would explore all avenues available to them once they've had an opportunity to review the board's findings.