Flannery and his band, the Lunatic Fringe, played in Redwood City, Mill Valley, Napa and Santa Cruz between Thursday and Sunday, with plans to deliver the money after the final concert, Flannery wrote on the band's Facebook page.
He thanked "all who have supported us, prayed for us and came to the shows," saying these were the last shows the band would play before Flannery heads to Giants spring training in Arizona next month.
The money will help with medical bills for Stow, a paramedic and father of two who suffered a serious head injury in the March 31, 2011, attack outside Dodger Stadium.
Months later, police arrested two men, Louie Sanchez and Marvin Norwood, who are awaiting trial.
Flannery was a coach for both of the Giants' 2010 and 2012 World Series wins, and collected $70,000 for Stow in a previous fundraising effort that included a large benefit concert in Napa last year with Bob Weir from the Grateful Dead.
Stow's family has posted regular updates on his recovery on the website www.support4bryanstow.com and said last Friday that he was back in the hospital with a large and serious blood clot in his leg.
The post stated that the doctor had told the family that "due to the size and hardness of the clot, he is surprised it didn't kill him."
The family said, "We are asking for some prayers right now. Bry has a huge support system (you!) and knowing that along with his strength and perseverance, he will get through this."