Owen Coyle's men - beaten 2-0 by the Gunners on Sunday - took a shock lead at the Emirates Stadium after seven minutes through Gary Cahill and Matthew Taylor then doubled the advantage from the penalty spot.
However, Arsenal rallied before half-time through Tomas Rosicky's strike.
Captain Cesc Fabregas netted a controversial equaliser on 52 minutes after Gallas had appeared to foul Mark Davies in the build-up, the midfielder left with a suspected broken ankle, and then Thomas Vermaelen completed the comeback.
Andrey Arshavin scored a fourth to take the Gunners above Chelsea on goals scored, albeit having now played a match more - but nevertheless a scenario which looked so unlikely following a resounding 3-0 home defeat by the Blues at the end of November which left Arsenal some 11 points adrift.
Wenger said: "Our mental and physical strength was tested again. We are certainly much more physically resistant.
"You cannot find a team better than Bolton in doing what they did tonight - they marked us man to man, didn't give us an inch of space. Physically, you are never better tested than against Bolton."
Gallas caught Davies on the ankle as the pair went for a 50/50 ball, but play was allowed to continue despite the Bolton protests as their man lay on the ground.
Arshavin battled to the edge of the area, where possession broke to Fabregas and he charged into the box before slipping a low angled drive through the keeper's legs.
There was a delay as Davies finally received treatment, and eventually had to be taken off on a stretcher, replaced by Gavin McCann.
The midfielder will have X-rays to determine the extent of the damage.
Wenger said: "I am sorry if the tackle was not good, and I apologise.
"However, to complain that we went on to play, I think that is unfair.
"The players did not even know what was happening behind them, whether the player has got up again or not.
"I don't believe you can kick the ball out every time a player is down when you win the ball. That is why they changed the rules.
"Remember (against) Everton, I did not think they should have kicked the ball out and it was a much more obvious situation because Denilson went down, they got the ball and might have gone 3-1 up.
"I said after the game that it was okay."
Wenger added: "We got some tackles, some big ones, but we had to cope with it.
"I am sorry if it is a foul, but it didn't look dirty from outside."
Coyle, however, was less than impressed by Gallas' challenge.
"The second goal was the big turning point," said Coyle, recently appointed after leaving Burnley.
"Clearly it was a foul, and closer to a red card. It was akin to assault and it changed the game.
"However, the fact is the referee has not seen it, and the lad is prostrate on the ground, and Arsenal being full of fair play as we keep hearing, have carried on scored an equaliser. That is hard to take.
"I don't want to sit here and make excuses, but I have seen red cards for less."