Ince was sent to the stands and did not appear for a press conference after the match, but his assistant Alex Rae explained the former England midfielder had sought out the female spectator and said sorry for the incident.
Goals from Neal Bishop and Ricardo Fuller earned league leaders Blackpool a 2-1 win on the south coast.
Ince watched from the stand behind the dugout as the visitors held out for their victory, which came despite them having full-back Jack Robinson sent off in the second half.
Fuller put Blackpool ahead after seven minutes, heading home Robinson's flick from a long throw, before Lewis Grabban scored his fifth goal of the season four minutes later to level the match.
Blackpool secured victory thanks to Bishop who headed home at the near post from a Tom Ince corner.
Ince senior was given his marching orders late in the second half.
Rae said: "Once we had an opportunity to score to make it 3-1 Paul threw a bottle on the ground and it bounced off the ground and into the crowd.
"The fourth official made a decision to send him to the stand so we just move on from it.
"We thought it was a bit harsh because it bounced through a barrier, but even still we're obviously not happy with it.
"To be fair the manager went over and apologised to the lady immediately as it actually hit her on the foot I think and she's accepted his apology."
Looking at the match, Rae said: "We are absolutely delighted at the win. Bournemouth are a very good team, have spent some money over the summer and are a very good passing team.
"To come (and win) here, which is obviously a difficult place because they've got a really good flowing system to the way they play, we are over the moon."
Bournemouth boss Howe was disappointed with his side's attacking display.
Despite substitute Wes Thomas going close and Brett Pitman having a goal ruled out for offside, his side struggled to create the chances to grab a second equaliser.
Howe said: "We reacted really well to the early goal and I thought for the first 20 minutes we were excellent and were in the ascendancy.
"They [Blackpool] defended very well, you can see why they've only conceded two goals prior to today's game. I thought their defensive performance was excellent.
"But you have to look at yourselves and I thought our attacking performance was below par. We're missing a lot of very good attacking players but there's no excuse for that, we needed to do better."