Boro looked to be cruising after first-half goals from Ishmael Miller and birthday boy Richard Smallwood but Blackpool hit back in a ding-dong second half, clawing one back through Wes Thomas before Scott McDonald restored Boro's lead.
Blackpool forced a second through Chris Basham then in a pivotal moment won a disputed penalty only for Jason Steele to save superbly from Thomas Ince. Boro sealed it late on through Adam Reach.
"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 penalty came when Jonathan Woodgate tackled Gary Taylor-Fletcher and although the referee waved play on the linesman persuaded him to alter his opinion.
"The frustration is that an official 70 yards away can overrule one 10 yards away without even having a discussion," said Mowbray.
"But in the 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."