As mixed-race groups were illegal under apartheid, the Blue Notes, increasingly harassed by authorities, emigrated to Europe in 1964, playing in France and Zürich, and eventually settling in London. After The Blue Notes split in the late 1960s, Pukwana joined McGregor's Brotherhood of Breathbig band, which again featured his soloing heavily. As a composer Pukwana wrote "Mra," one of the best-loved tunes by the Brotherhood. In February 1967, Pukwana received his first mention in America’s DownBeat magazine: "Tenorist Ronnie Scott’s Old Place, having a hard time breaking even, scored a financial success with the Bob Stuckey Trio, featuring the leader’s organ and altoist Dudu Pukwana". The trio later expanded to a quartet when Phil Lee joined on guitar,and this group performed twice on BBC's Jazz Club. As a quartet the band also had a regular session at the Witches Cauldron in Belsize Park. The band completed a series of UK dates throughout 1967, including regular appearances at Ronnie Scott's Jazz Club.
He also went on to form two groups with Feza and Moholo. The first was Assagai, an afro rock band that recorded for the Vertigo label. The second was Spear, with whom he recorded the seminal afro-jazz album In The Townships in 1973 for Virgin Records at The Manor Studio. Assagai and Spear, which recorded a few albums in the early 1970s, blended kwela rhythms, rocking guitars, and jazz solos. Pukwana's fiery voice was heard in many diverse settings including recordings of Mike Heron, Centipede and Toots and the Maytals as well as improvising with Misha Mengelberg and Han Bennink. With Mongezi Feza, Elton Dean, Keith Tippett, and Louis Moholo, Pukwana recorded two masterful acoustic tracks on the mostly electric album Diamond Express. The death of his great friend Mongezi Feza in 1975 also inspired the heart-rending "Blue Notes For Mongezi", alongside Blue Notes colleagues Johnny Dyani, Chris McGregor and Louis Moholo. He also guested on albums with his former Blue Notes colleague, Johnny Dyani, particularly Witchdoctor's Son, which features some of his best recorded work and played extensively with the drummer John Stevens. Several African leaders invited him into their groups, including Hugh Masekela and trombonist Jonas Gwangwa.
Zila and the later years
In 1978, Pukwana founded Jika Records and formed his own band, Zila, featuring South Africans Lucky Ranku on guitar and powerful vocalist Miss Pinise Saul. Zila recorded Zila Sounds, Live in Bracknell and Willisau, partly recorded at the Bracknell Jazz Festival, and Zila, the last with keyboardist Django Bates and Pukwana increasingly using soprano sax. In duo with John Stevens, he recorded the free session They Shoot to Kill, dedicated to Johnny Dyani. On 16 April 1990, Pukwana took part in the held at Wembley Stadium. He died in London of liver failure in June 1990, not long after the death of his longtime friend and colleague McGregor.