Ishmael Miller and Richard Smallwood put Boro ahead but Blackpool hit back through Wes Thomas before Scott McDonald extended Boro's lead. Blackpool forced a second through Chris Basham but Boro sealed it late on through Adam Reach after Jason Steele had saved Thomas Ince's penalty.
"It was a bit nervous in the second half and when we gave away the penalty it looked as if we would throw it all away but Jason made a truly fantastic save to keep us in front," said Mowbray.
"The frustration is that an official 70 yards away can over rule one 10 yards away without even having a discussion," said Mowbray. "That was a little strange. But in end it wasn't crucial because Jason made the save, we won the game, we got the three points and we move on.
"I was pleased because in the first half we played some fabulous football. It was as good as we have played all season. We knew they would come at us in the second half because we couldn't keep that level of play up and they had to gamble a bit."
Blackpool boss Michael Appleton was disappointed with his side's poor show in a one-sided first half.
"It was disappointing for myself and the staff and more so for the players because they were well short of how they can play.
"I've got to say I didn't see that first half coming. We improved in the second half and nearly did enough to get back into it.
"At the end of the day we are one excellent penalty save away from salvaging a game away at a side that are up at the top.
"When I took over people told me when Blackpool are good - very, very good - but when they are bad they are awful. I think in the first half I saw that bad side."