Greene, who claimed the 400m hurdles world crown in 2011, beat fellow Welshman Rhys Williams with a season's best run of 48.66seconds in Birmingham.
The 27-year-old was at the Alexander Stadium in a bid to find form, having qualified for next month's World Championships by virtue of being the reigning champion.
And he was pleased with the execution of his performance that left Williams in second despite a personal best, though he too has qualified for Moscow.
"I haven't been in top form so far and it was a really close race and exciting for the neutral so I was pleased to come away with victory," he said.
"I felt I went out fairly aggressively. Probably the middle part of my race was a bit slow so I pushed on a bit and managed to pick up a bit of speed and finished it off well.
"I need to carry on doing what I am doing in training - my times are coming down - and I know I will be in the right shape for Moscow."
Double Olympic medallist Christine Ohuruogu showed her pedigree to win over 400m, clocking 50.98 secs, while Marilyn Okoro got the better of rising star Jessica Judd to win the 800m title and James Wilkinson ended Luke Gunn's long domination of the men's 3,000m steeplechase.
"It feels fantastic. I just had to reverse last year, so I am really pleased," said Okoro.
"It was just about execution, I’m healthy and I had a great challenger in Jess Judd and I had to get her back for a couple of weeks ago and I am just so glad to have booked my place to Moscow. I ran for my life in that last ten metres."
Defending champion Yamile Aldama was forced to pull out of the women's triple jump, which was won in her absence by Laura Samuel.
Elsewhere, Emma Nuttall claimed the women's high jump, Andy Frost took the men's hammer, Rachel Wallader emerged victorious in the women's shot and Jade Lally won a third career women's discus national title.
Sainsbury’s British Championships is the second event in the Sainsbury’s Summer Series.