It further adds that it leaves large technology companies such as itself open to victimisation and attack from small "patent trolls", who use the threat of immediate shutdown orders to force out-of-court settlements for huge sums of money.
MercExchange counters that patents need to be properly protected and the current injunction system should be kept in place.
ebay claims that since the first 2003 court case it has sufficiently altered its "Buy it Now" tool to avoid breaching MercExchange's patents, but it remains to be seen what will be the final verdict of the Supreme Court.
The eBay versus MercExchange case comes three weeks after Research In Motion (RIM), the maker of the Blackberry email device, reached an out-of-court settlement in a similar patent dispute.
Canadian firm RIM faced the prospect of the Blackberry service being shut down in the US after American patent-holding company NTP said RIM had copied some of its technologies.
RIM eventually agreed to pay NTP $612.5m (£349m) to settle the dispute.
New precedent
The eBay versus MercExchange case is being closely watched by both the wider technology and pharmaceutical industries, as a verdict in favour of eBay would set a new precedent.
While other technology firms such as Amazon, Xerox and Time Warner have written to the Supreme Court in support of eBay, the drugs industry has sided with MercExchange's argument.
Patent lawyer Steve Maebius said the case could have a profound effect.
"Any time we talk about altering injunctions, we really are talking about altering the fundamental balance of power," he said.
The Supreme Court is expected to take several months before it reaches its verdict.
