He was unable to apply the finish, but had done enough to win the decision.
Woods beat Gonzalez on points in 2005 and was out to knock the Mexican out this time around.
"What a fighter this guy is," said Woods at ringside.
"I'm tough but he matched me all the way. It's a pleasure to be in with guys like this and to prove to Sheffield that boxing is the best sport there is.
"I thought I had him in the 11th round, but he came back. It was just a tough night."
Gonzalez, who had hoped to fight the rematch in Las Vegas, expressed disappointment with the judges' scorecards.
But he took some heart from his resilience.
"I wasn't hurt. I'm a warrior. He said he wanted to knock me out but he couldn't," he said.
"True warriors never die. They just keep coming back. He was going to go down, but I just ran out of time."
Saturday's fight was the first for Woods since a fine split-decision win over former undisputed champion Glen Johnson over a year ago.
Since that victory two years ago, the Yorkshire fighter has been dogged by an elbow injury.
"I found it hard to get my rhythm," Woods admitted.
"I've been out with elbow problems. I said it would be a tough fight. That will prepare for my next one.
"I'm a match for anybody and I'll look to be back in the ring in the next five to six months."
On the undercard, Huddersfield's
Mark Hobson
won back his old British cruiserweight title when referee Howard Foster stopped his bout with John 'Buster' Keeton in round four.
And Hornden heavyweight
John McDermott
got his career back on track with a 98-93 points win over Scott Gammer in an eliminator for a shot at current British heavyweight champion Danny Williams.