Manx rider Michael Evans, who claimed his first TT podium in race one, pulled over at Glen Helen with a mechanical issue on the first lap, as Dunlop led Todd and Adam McLean at the first timing sector by three seconds.
His advantage was up to eight seconds at Ramsey Hairpin, with Rob Hodson and Mike Browne slotting in ahead of McLean.
Dunlop held a 12-second lead over Todd at the pit stops, but lost six seconds to Todd in the service to put pressure on his advantage.
Behind the leading pair, Hodson, Browne, Herbertson and McLean were split by two-and-a-half seconds in the battle for third.
Dunlop soon restored and then extended his lead throughout the second lap, as he set a sector record from Glen Helen to Ballaugh Bridge, and Todd held a comfortable second.
The battle for third took a twist when race one podium sitter Hodson retired at the Gooseneck on the second lap, which promoted Herbertson into third ahead of Browne and McLean.
Dunlop ended the second lap 14.5 seconds up on Todd, while Herberston, who took his first TT podium in the class in 2024, held a 3.8 seconds advantage over Browne, with McLean, Paul Jordan and Barry Furber split by less than five seconds behind.
After being overtaken on the road by Dunlop, Jordan, who was the first bike down Bray Hill, started flying into podium contention by slipstreaming behind the race leader.
Northern Ireland’s Jordan managed to complete the lap tucked in behind Dunlop, but fell just short of his podium bid as Herbertson claimed third by 3.141 seconds for his second-ever TT rostrum.
Todd was a lonely second for his fifth podium of the TT, while Herbertson was emotional after racing onto the podium after a last-ditch effort to make the event after his original plans fell through.
“To do it twice, it’s fantastic,” England’s Herbertson told TT Plus.
“Doing that last lap, I was praying to everyone ‘please make it home’. I’m over the moon.
“It’s been bananas. Five and a half weeks to turn it around to get to the TT, thanks to friends and even strangers.
“Strangers saying, ‘I want to see you there’. To get back on the box, I hope they’re proud.”
