Rachubka, on loan from Leeds, kept out Warren Feeney's penalty with just 12 minutes left after Michael Liddle was adjudged to have brought down substitute Paris Cowan-Hall. But he was then sent off in injury time after reacting when Feeney followed up a loose ball and challenged him.
Plymouth's Luke Young made a lively start with a strike that had to be tipped round a post by Rachubka early on.
However, it looked like Stanley would open the scoring but keeper Rene Gilmartin produced a superb stop to keep out a Lee Molyneux free-kick before then denying Rommy Boco.
A disputed free-kick after 27 minutes saw Plymouth take the lead. Robbie Williams' 30-yard effort crashed against a post and bounced nicely for winger Onismor Bhasera to finish off.
Stanley had chances to get back on level terms as Gilmartin denied Molyneux again and, on the stroke of half-time, Craig Lindfield was one-on-one with the keeper but Gilmartin kept the hosts out again.
They finally found a way past Gilmartin after 50 minutes when a high ball into the box was not cleared by the Pilgrims defence and it fell into Jame Beattie's path. The former England man walloped a low shot into the net from 12 yards out.
Gilmartin then denied Luke Joyce from a free-kick as Stanley piled on the pressure and the keeper somehow clawed out the follow-up to keep it all-square.
Then came the penalty, with Rachubka saving with his legs. And there was time for Stanley to then grab it late on but Gilmartin spectacularly kept out Joyce's free-kick.
Darren Purse hit the crossbar in the dying minutes for Plymouth and then came the late brawl in injury time which saw the Stanley keeper see red.