Hartley denied that he had been involved in any incident at Franklin's Gardens but television footage has showed how he and Best clashed in the 64th minute, although Best was not hurt in the incident.
The charge carries a ban of between two and eight weeks but Hartley's troubled past could count against him if he is found guilty.
Hartley served a six-month suspension for gouging back in 2007 and was brought to justice for biting the finger of Ireland and Lions flanker Stephen Ferris during England's Six Nations win at Twickenham in March of this year.
The New Zealand born star was banned for eight weeks for that indiscretion, although glowing character references from England assistant Graham Rowntree and Saints boss Jim Malinder ensured he had his punishment reduced from 12 weeks for five years' good behaviour.
Hartley and his supporters have always said that he is given a raw deal regarding his discipline because of the two high-profile incidents that will always follow him around but this latest allegation won't do anything to dismiss suggestions that he is too hot headed to wear the Lions No2 jersey against the Wallabies next summer.
"Hartley is alleged to have struck Ulster Rugby forward, Rory Best with his arm," read a statement from Heineken Cup organisers ERC.
"Details of the hearing date and the appointed independent Judicial Officer will be announced shortly.
"10.4(a) Punching or striking. A player must not strike an opponent with the fist or arm, including the elbow, shoulder, head or knee(s).
"Under the IRB Recommended Sanctions for Offences Committed within the Playing Enclosure, Law 10.4 (a) carries the following penalties: Low End: 2 weeks; Mid Range: 5 weeks; Top End: 8+ to 52 weeks."