The Australian pair led the event heading into the final day hour long Madison and responded after repeated challenges to hold their position before Cavendish and Kennaugh launched their final attempt to take the title.
Meyer and Scotson held on for the win while Belgians Kenny de Ketele and Moreno de Pauw rounded out the podium after winning last year.
“I’ve achieved some good things, some rainbow bands but this is an honourable event to put on the palmares,” Meyer said.
“I’m loving my track cycling again, I’ve got some big targets over the next three years and I’m sure I’ll meet these guys again.
“Possibly at an Olympic Games now that the Madison is back in, so it’s going to be big three years and I can’t wait for what’s ahead.”
Scotson detailed the pressure applied by the British duo but noted it was not unexpected given their pedigree.
“We knew coming up against such big stars, they were always going to throw it at us all the way up to the line.
“We were prepared for that, we just had to fight and fight. Every time they got a lap back on us in that final Madison we had to go again no matter how tired we were, but it paid off in the end.
“The last attack from Cavendish and Kennaugh definitely added a few nerves, when Cav takes off he’s one of the fastest in the world.
“He opened up that gap real quick, we had to try and stay calm. We knew we had them on the back foot and we couldn’t give them too much road, eventually, we had the legs to hold on and it feels so good to win a Six Day London.”
Cavendish who finished second in 2016 with now-retired partner Bradley Wiggins, was satisfied with the result despite the unsuccessful raid.
“We just had to put all our chips on the table, we tried to get it back and kept getting it back but every time we went they just had us,” Cavendish said.
“I said to Pete as soon as the lap board came down, let’s put all our chips in the centre after 20 laps and go for broke."